diff options
Diffstat (limited to 'gnu/packages/graph.scm')
| -rw-r--r-- | gnu/packages/graph.scm | 180 |
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."))) |