;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;;
;;; This file is part of GNU Guix.
;;;
(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 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
(define-public r-igraph
(package
(name "r-igraph")
- (version "1.1.2")
+ (version "1.2.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "igraph" version))
(sha256
(base32
- "1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9"))))
+ "0scrbqb26pam8akblb4g9rkz888s0xffw3gcly78s4ijj67barxd"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(inputs
`(("gmp" ,gmp)
- ("libxml2" ,libxml2)))
+ ("glpk" ,glpk)
+ ("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
(propagated-inputs
- `(("r-irlba" ,r-irlba)
- ("r-magrittr" ,r-magrittr)
+ `(("r-magrittr" ,r-magrittr)
("r-matrix" ,r-matrix)
("r-pkgconfig" ,r-pkgconfig)))
(home-page "http://igraph.org")
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 "2.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rgraphviz" version))
+ (sha256
+ (base32
+ "00lrkbgbb4payybckcmazsv8skysgdlglyqbl7yjb37vv3gnfc6c"))))
+ (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 "http://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+)))
HCoop / jackhill / guix / guix.git / blobdiff