gnu: volk: Fetch from git repository. - guix

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author	Tobias Geerinckx-Rice <me@tobias.gr>	2020-11-25 21:11:00 +0100
committer	Tobias Geerinckx-Rice <me@tobias.gr>	2020-11-25 23:56:28 +0100
commit	fc14661c7b23d93d4fd3e2eacbbfc8dbe10807c5 (patch)
tree	6c2cf420c9a917554ffd86a752c3b21a00afde76 /gnu
parent	8b928a3931cafddb291152bc259b634ab3ab441b (diff)
download	guix-fc14661c7b23d93d4fd3e2eacbbfc8dbe10807c5.tar.gz guix-fc14661c7b23d93d4fd3e2eacbbfc8dbe10807c5.zip

gnu: volk: Fetch from git repository.

* gnu/packages/engineering.scm (volk)[source]: Use GIT-FETCH and GIT-FILE-NAME.

Diffstat (limited to 'gnu')

-rw-r--r--

gnu/packages/engineering.scm

1 files changed, 6 insertions, 4 deletions

;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017, 2018, 2019, 2020, 2022, 2023 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2021, 2022 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> ;;; Copyright © 2021, 2023 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org> ;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2022 Marius Bakke <marius@gnu.org> ;;; ;;; 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 gexp) #: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 pyproject) #: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 autotools) #:use-module (gnu packages bioconductor) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cran) #:use-module (gnu packages datastructures) #:use-module (gnu packages gd) #:use-module (gnu packages graphics) #:use-module (gnu packages graphviz) #:use-module (gnu packages gtk) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #: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 plfit (package (name "plfit") (version "0.9.4") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/ntamas/plfit") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "042b60cnsz5wy27sz026xs0mnn9p58j46crgs78skncgkvzqyyc6")))) (build-system cmake-build-system) (arguments '(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON"))) (home-page "https://github.com/ntamas/plfit") (synopsis "Tool for fitting power-law distributions to empirical data") (description "The @command{plfit} command fits power-law distributions to empirical (discrete or continuous) data, according to the method of Clauset, Shalizi and Newman (@cite{Clauset A, Shalizi CR and Newman MEJ: Power-law distributions in empirical data. SIAM Review 51, 661-703 (2009)}).") (license license:gpl2+))) (define-public igraph (package (name "igraph") (version "0.10.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/igraph/igraph/releases/" "download/" version "/igraph-" version ".tar.gz")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-26))) (snippet '(begin ;; igraph insists on building its own copy of CxSparse ;; (see: https://github.com/igraph/igraph/commit/\ ;; 334318b7dfe46501236272ca336580f4748114b0) and the build ;; has no support to use a system provided 'pcg'. (define keep-libraries '("cs" "pcg")) (define keep (append '("." ".." "CMakeLists.txt") keep-libraries)) (define keep? (cut member <> keep)) (with-directory-excursion "vendor" (for-each delete-file-recursively (scandir "." (negate keep?)))) (call-with-output-file "vendor/CMakeLists.txt" (cut format <> "~{add_subdirectory(~a)~%~}" keep-libraries)) (substitute* '("src/CMakeLists.txt" "etc/cmake/benchmark_helpers.cmake") ;; Remove extraneous bundling related variables. ((".*_IS_VENDORED.*") "")))) (sha256 (base32 "1z1ay3l1h64jc2igbl2ibvi20sswy56v2yk3ykhis7jzijsh0mxa")))) (build-system cmake-build-system) (arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON") #:test-target "check")) (native-inputs (list pkg-config)) (inputs (list arpack-ng gmp glpk libxml2 lapack openblas plfit)) ;; libxml2 is in the 'Requires.private' of igraph.pc. (propagated-inputs (list libxml2)) (home-page "https://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 ;; Temporarily use a precise commit, as there was a mistake in the last ;; release that was fixed by it (see: ;; https://github.com/igraph/python-igraph/issues/632). (let ((revision "0") (commit "b6ebd8eb277fc1d0e33340a6624629a10c638992")) (package (inherit igraph) (name "python-igraph") (version (git-version "0.10.4" revision commit)) (source (origin (method git-fetch) ;; The PyPI archive lacks tests. (uri (git-reference (url "https://github.com/igraph/python-igraph") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0dhrz5a6pi6vs94fm8q4nmkh6v1nmpw1sk482xls213zcbbh67hd")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'unpack 'specify-libigraph-location (lambda _ (let ((igraph #$(this-package-input "igraph"))) (substitute* "setup.py" (("(LIBIGRAPH_FALLBACK_INCLUDE_DIRS = ).*" _ var) (string-append var (format #f "[~s]~%" (string-append igraph "/include/igraph")))) (("(LIBIGRAPH_FALLBACK_LIBRARY_DIRS = ).*" _ var) (string-append var (format #f "[~s]~%" (string-append igraph "/lib"))))))))))) (inputs (list igraph)) (propagated-inputs (list python-texttable)) (native-inputs (list python-pytest)) (home-page "https://igraph.org/python/") (synopsis "Python bindings for the igraph network analysis library")))) (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") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z")))) (build-system r-build-system) (propagated-inputs (list 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 "5.14.1") (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 "12iy5cswn5c0590fvl87nr6vfyhvbxymrldh4c7dfm2gn6h8z8w0")))) (build-system python-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-before 'build 'skip-npm ;; npm is not packaged so build without it (lambda _ (setenv "SKIP_NPM" "T"))) (add-after 'unpack 'fix-version ;; TODO: Versioneer in Guix gets its release version from the ;; parent directory, but the plotly package is located inside a ;; depth 3 subdirectory. Try to use versioneer if possible. (lambda _ (substitute* "packages/python/plotly/setup.py" (("version=versioneer.get_version\$),") (format #f "version=~s," #$version))) (substitute* "packages/python/plotly/plotly/version.py" (("__version__ = get_versions\\(\$\\[\"version\"\\]") (format #f "__version__ = ~s" #$version))))) (add-after 'fix-version 'chdir (lambda _ (chdir "packages/python/plotly"))) (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"))))))) (native-inputs (list python-ipywidgets python-pytest python-xarray)) (propagated-inputs (list python-ipython python-pandas python-pillow python-requests python-retrying python-six python-tenacity 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 plots, area charts, bar charts, error bars, box plots, histograms, heatmaps, 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 (list python-decorator python-nbformat python-pandas python-pytz python-requests python-six)) (arguments (list #:tests? #false ;The tests are not distributed in the release #:phases '(modify-phases %standard-phases (add-after 'unpack 'python-compatibility (lambda _ (substitute* "plotly/grid_objs/grid_objs.py" (("from collections import MutableSequence") "from collections.abc import MutableSequence"))))))))) (define-public python-louvain (package (name "python-louvain") (version "0.16") (source (origin (method url-fetch) (uri (pypi-uri "python-louvain" version)) (patches (search-patches "python-louvain-fix-test.patch")) (sha256 (base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp")))) (build-system python-build-system) (native-inputs (list python-setuptools-57)) ;for use_2to3 support (propagated-inputs (list python-networkx python-numpy)) (home-page "https://github.com/taynaud/python-louvain") (synopsis "Louvain algorithm for community detection") (description "This package provides a pure Python implementation of the Louvain algorithm for community detection in large networks.") (license license:bsd-3))) (define-public python-vtraag-louvain (package (name "python-vtraag-louvain") (version "0.8.0") (source (origin (method url-fetch) (uri (pypi-uri "louvain" version)) (sha256 (base32 "16l2zi4jwc3vpvpnz32jv7xy0g5087dp9y57wxplj1xa9r312x0i")))) (build-system pyproject-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'do-not-use-bundled-igraph (lambda _ (substitute* "setup.py" (("self.external = False") "self.external = True") (("self.use_pkgconfig = False") "self.use_pkgconfig = True"))))))) (inputs (list igraph)) (propagated-inputs (list python-igraph)) (native-inputs (list pkg-config python-ddt python-setuptools-scm)) (home-page "https://github.com/vtraag/louvain") (synopsis "Community detection in large networks") (description "Louvain is a general algorithm for methods of community detection in large networks.") (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 (list openblas)) (native-inputs (list 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~a/ -I~a/lib/python~a/site-packages/numpy/core/include LIBS = -lpython~a -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 (list python-matplotlib 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 "0.9.1") (source (origin (method url-fetch) (uri (pypi-uri "leidenalg" version)) (sha256 (base32 "1wvmi6ca9kf8pbxg6b18n64h82wr9a6wcdazyn82pww0dwxzwp3y")))) (build-system python-build-system) (arguments '(#:tests? #f ;tests are not included #:phases (modify-phases %standard-phases (add-after 'unpack 'fix-requirements (lambda _ (substitute* "setup.py" (("self.external = False") "self.external = True") (("self.use_pkgconfig = False") "self.use_pkgconfig = True") (("python-igraph >=") "igraph >="))))))) (native-inputs (list pkg-config python-setuptools-scm)) (inputs (list igraph)) (propagated-inputs (list 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 "3.0.2.0") (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 "1c7bnxgiz28mqsq3a3msznmjq629w0qqjynm2rqnnjn2qpc22h3i")))) (build-system gnu-build-system) (native-inputs (list autoconf automake 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 "0.9") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/rankwidth/" "rw-" version ".tar.gz")) (sha256 (base32 "0hdlxxmlccb6fp7g58zv0rdzpbyjn9bgqlf052sgrk95zq33bq61")) (patches (search-patches "rw-igraph-0.10.patch")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) (inputs (list 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 (list pkg-config)) (inputs (list gd)) (home-page "https://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+))) (define-public python-graph-tool (package (name "python-graph-tool") (version "2.46") (source (origin (method url-fetch) (uri (string-append "https://downloads.skewed.de/graph-tool/graph-tool-" version ".tar.bz2")) (sha256 (base32 "0x9jgnq9xcja3q954y7nhdzd374p4h203pymxh51b6lqqbq0hm9h")))) (build-system gnu-build-system) (arguments `(#:imported-modules (,@%gnu-build-system-modules (guix build python-build-system)) #:modules (,@%gnu-build-system-modules ((guix build python-build-system) #:select (site-packages))) #:configure-flags (list (string-append "--with-boost=" (assoc-ref %build-inputs "boost")) (string-append "--with-python-module-path=" (site-packages %build-inputs %outputs))))) (native-inputs (list ncurses pkg-config)) (inputs (list boost cairomm-1.14 cgal expat gmp gtk+ python-wrapper sparsehash)) (propagated-inputs (list python-matplotlib python-numpy python-pycairo python-scipy)) (synopsis "Manipulate and analyze graphs with Python efficiently") (description "Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other Python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library.") (home-page "https://graph-tool.skewed.de/") (license license:lgpl3+)))


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