;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019, 2021 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>
;;;
;;; This file is part of GNU Guix.
;;;
#: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 "0.7.1")
+ (version "0.8.4")
(source
(origin
(method url-fetch)
- (uri (string-append "http://igraph.org/nightly/get/c/igraph-"
- version ".tar.gz"))
+ (uri (string-append "https://github.com/igraph/igraph/releases/"
+ "download/" version "/igraph-" version ".tar.gz"))
(sha256
- (base32
- "1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
+ (base32 "127q6q40kbmvd62yhbz6dlfk370qiq98s1iscyagpgbpjwb4xvyf"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
- (list "--with-external-glpk"
+ (list "--disable-static"
+ "--with-external-glpk"
"--with-external-blas"
"--with-external-lapack")))
(inputs
("lapack" ,lapack)
("openblas" ,openblas)
("zlib" ,zlib)))
- (home-page "http://igraph.org")
+ (home-page "https://igraph.org")
(synopsis "Network analysis and visualization")
(description
"This package provides a library for the analysis of networks and graphs.
(define-public python-igraph
(package (inherit igraph)
(name "python-igraph")
- (version "0.7.1.post6")
+ (version "0.8.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "python-igraph" version))
(sha256
- (base32
- "0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
+ (base32 "0wkxrs28qdvnrz7d4jzcf2bh6v2yqzx3wyfziihfgsi2gn6n60a6"))))
(build-system python-build-system)
- (arguments '())
+ (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)))
- (native-inputs
- `(("pkg-config" ,pkg-config)))
- (home-page "http://pypi.python.org/pypi/python-igraph")
- (synopsis "Python bindings for the igraph network analysis library")))
-
-(define-public r-igraph
- (package
- (name "r-igraph")
- (version "1.2.2")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "igraph" version))
- (sha256
- (base32
- "1bggm7b8v3bh7q2589w26qvd7sgs69m4qiij7d0rbm0ykkgxm8lx"))))
- (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 "1.1-0.1")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "diffusionMap" version))
- (sha256
- (base32
- "11l4kbciawvli5nlsi4qaf8afmgk5xgqiqpdyhvaqri5mx0zhk5j"))))
- (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 "2.26.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rgraphviz" version))
- (sha256
- (base32
- "0bp6517xsih0wng2rgkh9z4r1afqhwl3h04z6ssm7p4cdj0ahm4y"))))
- (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)))
+ `(("python-texttable" ,python-texttable)))
(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)))
+ `(("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-rbiofabric
(let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/wjrl/RBioFabric.git")
+ (url "https://github.com/wjrl/RBioFabric")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(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"))))
+ (version "4.14.3")
+ (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
+ "02wlgy7gf3v5ckiq9ab3prm53cckxkavlghqgkk9xw2sfmmrn61q"))))
(build-system python-build-system)
(arguments
- '(#:tests? #f)) ; The tests are not distributed in the release
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _
+ (chdir "packages/python/plotly")
+ #t))
+ (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"))
+ #t))
+ (add-before 'reset-gzip-timestamps 'make-files-writable
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (for-each (lambda (file) (chmod file #o644))
+ (find-files out "\\.gz"))
+ #t))))))
+ (native-inputs
+ `(("python-ipywidgets" ,python-ipywidgets)
+ ("python-pytest" ,python-pytest)
+ ("python-xarray" ,python-xarray)))
(propagated-inputs
- `(("python-decorator" ,python-decorator)
- ("python-nbformat" ,python-nbformat)
+ `(("python-ipython" ,python-ipython)
("python-pandas" ,python-pandas)
- ("python-pytz" ,python-pytz)
+ ("python-pillow" ,python-pillow)
("python-requests" ,python-requests)
- ("python-six" ,python-six)))
- (home-page "https://plot.ly/python/")
+ ("python-retrying" ,python-retrying)
+ ("python-six" ,python-six)
+ ("python-statsmodels" ,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
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
+ `(("python-decorator" ,python-decorator)
+ ("python-nbformat" ,python-nbformat)
+ ("python-pandas" ,python-pandas)
+ ("python-pytz" ,python-pytz)
+ ("python-requests" ,python-requests)
+ ("python-six" ,python-six)))
+ (arguments
+ '(#:tests? #f)))) ; The tests are not distributed in the release
+
(define-public python2-plotly
- (package-with-python2 python-plotly))
+ (package-with-python2 python-plotly-2.4.1))
+
+(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")
+ (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")
+ (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+)))
HCoop / jackhill / guix / guix.git / blobdiff