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-rw-r--r--gnu/packages/graph.scm180
1 files changed, 178 insertions, 2 deletions
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 7ed13d37c7..5bcc48dbe6 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -2,6 +2,7 @@
;;; 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>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -22,6 +23,8 @@
#: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)
@@ -30,6 +33,7 @@
#:use-module (gnu packages gcc)
#: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)
@@ -40,6 +44,7 @@
#: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))
@@ -100,14 +105,14 @@ more.")
(define-public r-igraph
(package
(name "r-igraph")
- (version "1.2.4")
+ (version "1.2.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "igraph" version))
(sha256
(base32
- "1jwjjl0l4054w05bik17p2d6rj3lx68iv716phajhnbbmckfnj0h"))))
+ "1074y8mvprrqlkb4vwa2qc9l03r8d7p5vaaqacj4ljjs7dvcq6l9"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -239,3 +244,174 @@ subplots, multiple-axes, polar charts, and bubble charts. ")
(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 -std=c++11 -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.")))