mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-11-07 07:26:13 -05:00
548 lines
21 KiB
Scheme
548 lines
21 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
|
|
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
|
|
;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
|
|
;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
|
|
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
|
|
;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
|
|
;;;
|
|
;;; 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 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 python)
|
|
#:use-module (guix build-system r)
|
|
#:use-module ((guix licenses) #:prefix license:)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages gcc)
|
|
#:use-module (gnu packages autotools)
|
|
#:use-module (gnu packages bioconductor)
|
|
#:use-module (gnu packages bioinformatics)
|
|
#:use-module (gnu packages check)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages cran)
|
|
#:use-module (gnu packages gd)
|
|
#:use-module (gnu packages graphviz)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages multiprecision)
|
|
#:use-module (gnu packages pkg-config)
|
|
#:use-module (gnu packages python)
|
|
#: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 igraph
|
|
(package
|
|
(name "igraph")
|
|
(version "0.8.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://github.com/igraph/igraph/releases/"
|
|
"download/" version "/igraph-" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "0wbvrac3ip3lqmbkckhnxa2swlbc86l1h8mazdlb618kx3winvi6"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list "--with-external-glpk"
|
|
"--with-external-blas"
|
|
"--with-external-lapack")))
|
|
(inputs
|
|
`(("gmp" ,gmp)
|
|
("glpk" ,glpk)
|
|
("libxml2" ,libxml2)
|
|
("lapack" ,lapack)
|
|
("openblas" ,openblas)
|
|
("zlib" ,zlib)))
|
|
(home-page "http://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
|
|
(package (inherit igraph)
|
|
(name "python-igraph")
|
|
(version "0.8.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "python-igraph" version))
|
|
(sha256
|
|
(base32
|
|
"13mbrlmnbgbzw6y8ws7wj0a3ly3in8j4l1ngi6yxvgvxxi4bprj7"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:configure-flags
|
|
(list "--use-pkg-config")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'build
|
|
(lambda _
|
|
(invoke "python" "./setup.py" "build" "--use-pkg-config")))
|
|
(delete 'check)
|
|
(add-after 'install 'check
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(add-installed-pythonpath inputs outputs)
|
|
(invoke "pytest" "-v"))))))
|
|
(inputs
|
|
`(("igraph" ,igraph)))
|
|
(propagated-inputs
|
|
`(("python-texttable" ,python-texttable)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)
|
|
("python-pytest" ,python-pytest)))
|
|
(home-page "https://pypi.org/project/python-igraph/")
|
|
(synopsis "Python bindings for the igraph network analysis library")))
|
|
|
|
(define-public r-igraph
|
|
(package
|
|
(name "r-igraph")
|
|
(version "1.2.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "igraph" version))
|
|
(sha256
|
|
(base32
|
|
"126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(inputs
|
|
`(("gmp" ,gmp)
|
|
("glpk" ,glpk)
|
|
("libxml2" ,libxml2)
|
|
("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-magrittr" ,r-magrittr)
|
|
("r-matrix" ,r-matrix)
|
|
("r-pkgconfig" ,r-pkgconfig)))
|
|
(home-page "http://igraph.org")
|
|
(synopsis "Network analysis and visualization")
|
|
(description
|
|
"This package provides routines for simple graphs and network analysis.
|
|
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 r-diffusionmap
|
|
(package
|
|
(name "r-diffusionmap")
|
|
(version "1.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "diffusionMap" version))
|
|
(sha256
|
|
(base32
|
|
"1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
|
|
(properties `((upstream-name . "diffusionMap")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-igraph" ,r-igraph)
|
|
("r-matrix" ,r-matrix)
|
|
("r-scatterplot3d" ,r-scatterplot3d)))
|
|
(home-page "https://www.r-project.org")
|
|
(synopsis "Diffusion map")
|
|
(description "This package implements the diffusion map method of data
|
|
parametrization, including creation and visualization of diffusion maps,
|
|
clustering with diffusion K-means and regression using the adaptive regression
|
|
model.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rgraphviz
|
|
(package
|
|
(name "r-rgraphviz")
|
|
(version "2.32.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (bioconductor-uri "Rgraphviz" version))
|
|
(sha256
|
|
(base32
|
|
"1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
|
|
(properties `((upstream-name . "Rgraphviz")))
|
|
(build-system r-build-system)
|
|
;; FIXME: Rgraphviz bundles the sources of an older variant of
|
|
;; graphviz. It does not build with the latest version of graphviz, so
|
|
;; we do not add graphviz to the inputs.
|
|
(inputs `(("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-graph" ,r-graph)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "https://bioconductor.org/packages/Rgraphviz")
|
|
(synopsis "Plotting capabilities for R graph objects")
|
|
(description
|
|
"This package interfaces R with the graphviz library for plotting R graph
|
|
objects from the @code{graph} package.")
|
|
(license license:epl1.0)))
|
|
|
|
(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.git")
|
|
(commit commit)))
|
|
(file-name (string-append name "-" version "-checkout"))
|
|
(sha256
|
|
(base32
|
|
"1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-igraph" ,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 "2.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "plotly" version))
|
|
(sha256
|
|
(base32
|
|
"0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:tests? #f)) ; The tests are not distributed in the release
|
|
(propagated-inputs
|
|
`(("python-decorator" ,python-decorator)
|
|
("python-nbformat" ,python-nbformat)
|
|
("python-pandas" ,python-pandas)
|
|
("python-pytz" ,python-pytz)
|
|
("python-requests" ,python-requests)
|
|
("python-six" ,python-six)))
|
|
(home-page "https://plot.ly/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 python2-plotly
|
|
(package-with-python2 python-plotly))
|
|
|
|
(define-public python-louvain
|
|
(package
|
|
(name "python-louvain")
|
|
(version "0.6.1")
|
|
;; The tarball on Pypi does not include the tests.
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/vtraag/louvain-igraph.git")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
`(("python-ddt" ,python-ddt)
|
|
("python-igraph" ,python-igraph)))
|
|
(inputs
|
|
`(("igraph" ,igraph)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)
|
|
("python-pytest" ,python-pytest)))
|
|
(home-page "https://github.com/vtraag/louvain-igraph")
|
|
(synopsis "Algorithm for methods of community detection in large networks")
|
|
(description
|
|
"This package provides an implementation of the Louvain algorithm for use
|
|
with igraph. Louvain is a general algorithm for methods of community
|
|
detection in large networks.
|
|
|
|
This package has been superseded by the @code{leidenalg} package and should
|
|
not be used for new projects.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public faiss
|
|
(package
|
|
(name "faiss")
|
|
(version "1.5.0")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/facebookresearch/faiss.git")
|
|
(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
|
|
`(("openblas" ,openblas)))
|
|
(native-inputs
|
|
`(("googletest" ,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~am/ -I~a/lib/python~a/site-packages/numpy/core/include
|
|
LIBS = -lpython~am -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
|
|
`(("python-matplotlib" ,python-matplotlib)
|
|
("python-numpy" ,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 "0.7.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "leidenalg" version))
|
|
(sha256
|
|
(base32
|
|
"15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
|
|
(build-system python-build-system)
|
|
(arguments '(#:tests? #f)) ; tests are not included
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("igraph" ,igraph)))
|
|
(propagated-inputs
|
|
`(("python-igraph" ,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 "3.0.0.5")
|
|
(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
|
|
"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+)))
|
|
|
|
(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
|
|
`(("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("gd" ,gd)))
|
|
(home-page "http://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+)))
|