diff options
Diffstat (limited to 'gnu/packages/graph.scm')
| -rw-r--r-- | gnu/packages/graph.scm | 265 |
1 files changed, 153 insertions, 112 deletions
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index c9486935ae..de68ff78b1 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -8,6 +8,8 @@ ;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com> ;;; Copyright © 2021 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org> +;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2022 Marius Bakke <marius@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -26,6 +28,7 @@ (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) @@ -35,7 +38,6 @@ #: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) @@ -61,31 +63,72 @@ #:use-module (gnu packages time) #:use-module (gnu packages xml)) +(define-public plfit + (package + (name "plfit") + (version "0.9.3") + (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 + "03x5jbvg8vwr92682swy58ljxrhqwmga1xzd0cpfbfmda41gm2fb")))) + (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 "0.8.4") + (version "0.9.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/igraph/igraph/releases/" "download/" version "/igraph-" version ".tar.gz")) + (modules '((guix build utils))) + (snippet '(begin + ;; Fully unbundle igraph (see: + ;; https://github.com/igraph/igraph/issues/1897). + (delete-file-recursively "vendor") + (substitute* "CMakeLists.txt" + (("add_subdirectory\\(vendor\\).*") + "")) + ;; Help CMake to find our plfit headers. + (substitute* "etc/cmake/FindPLFIT.cmake" + (("^ NAMES plfit.h.*" all) + (string-append all + " PATH_SUFFIXES plfit"))) + (substitute* '("src/CMakeLists.txt" + "etc/cmake/benchmark_helpers.cmake") + ;; Remove bundling related variables. + ((".*_IS_VENDORED.*") + "")))) (sha256 - (base32 "127q6q40kbmvd62yhbz6dlfk370qiq98s1iscyagpgbpjwb4xvyf")))) - (build-system gnu-build-system) + (base32 "11zkj9bpqcadb0rc4ahvjp9047dp9hna8cn3b0vl3zpc9v2rwabw")))) + (build-system cmake-build-system) (arguments - `(#:configure-flags - (list "--disable-static" - "--with-external-glpk" - "--with-external-blas" - "--with-external-lapack"))) + '(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON"))) + (native-inputs (list pkg-config)) (inputs - `(("gmp" ,gmp) - ("glpk" ,glpk) - ("libxml2" ,libxml2) - ("lapack" ,lapack) - ("openblas" ,openblas) - ("zlib" ,zlib))) + (list arpack-ng + gmp + glpk + libxml2 + lapack + openblas + plfit + suitesparse)) (home-page "https://igraph.org") (synopsis "Network analysis and visualization") (description @@ -96,37 +139,47 @@ more.") (license license:gpl2+))) (define-public python-igraph - (package (inherit igraph) + (package + (inherit igraph) (name "python-igraph") - (version "0.8.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "python-igraph" version)) - (sha256 - (base32 "0wkxrs28qdvnrz7d4jzcf2bh6v2yqzx3wyfziihfgsi2gn6n60a6")))) + (version "0.9.9") + (source (origin + (method git-fetch) + ;; The PyPI archive lacks tests. + (uri (git-reference + (url "https://github.com/igraph/python-igraph") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ravcww2jcr8fgi97gdxv00s5nkx59ljxy928nnniyd0231bqwlc")))) (build-system python-build-system) (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")))))) + (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")))))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-v"))))))) (inputs - `(("igraph" ,igraph))) + (list igraph)) (propagated-inputs - `(("python-texttable" ,python-texttable))) + (list python-texttable)) (native-inputs - `(("pkg-config" ,pkg-config) - ("python-pytest" ,python-pytest))) - (home-page "https://pypi.org/project/python-igraph/") + (list python-pytest)) + (home-page "https://igraph.org/python/") (synopsis "Python bindings for the igraph network analysis library"))) (define-public r-rbiofabric @@ -146,7 +199,7 @@ more.") "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z")))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph))) + (list r-igraph)) (home-page "http://www.biofabric.org/") (synopsis "BioFabric network visualization") (description "This package provides an implementation of the function @@ -183,32 +236,23 @@ lines.") (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)))))) + (invoke "pytest" "_plotly_utils/tests"))))))) (native-inputs - `(("python-ipywidgets" ,python-ipywidgets) - ("python-pytest" ,python-pytest) - ("python-xarray" ,python-xarray))) + (list python-ipywidgets python-pytest python-xarray)) (propagated-inputs - `(("python-ipython" ,python-ipython) - ("python-pandas" ,python-pandas) - ("python-pillow" ,python-pillow) - ("python-requests" ,python-requests) - ("python-retrying" ,python-retrying) - ("python-six" ,python-six) - ("python-statsmodels" ,python-statsmodels))) + (list python-ipython + python-pandas + python-pillow + python-requests + python-retrying + python-six + 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. ") +subplots, multiple-axes, polar charts, and bubble charts.") (license license:expat))) (define-public python-plotly-2.4.1 @@ -223,12 +267,12 @@ subplots, multiple-axes, polar charts, and bubble charts. ") "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))) + (list python-decorator + python-nbformat + python-pandas + python-pytz + python-requests + python-six)) (arguments '(#:tests? #f)))) ; The tests are not distributed in the release @@ -243,9 +287,10 @@ subplots, multiple-axes, polar charts, and bubble charts. ") (sha256 (base32 "1sqp97fwh4asx0jr72x8hil8z8fcg2xq92jklmh2m599pvgnx19a")))) (build-system python-build-system) + (native-inputs + (list python-setuptools)) ;for use_2to3 support (propagated-inputs - `(("python-networkx" ,python-networkx) - ("python-numpy" ,python-numpy))) + (list python-networkx python-numpy)) (home-page "https://github.com/taynaud/python-louvain") (synopsis "Louvain algorithm for community detection") (description @@ -269,13 +314,11 @@ algorithm for community detection in large networks.") "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k")))) (build-system python-build-system) (propagated-inputs - `(("python-ddt" ,python-ddt) - ("python-igraph" ,python-igraph))) + (list python-ddt python-igraph)) (inputs - `(("igraph" ,igraph))) + (list igraph)) (native-inputs - `(("pkg-config" ,pkg-config) - ("python-pytest" ,python-pytest))) + (list pkg-config python-pytest)) (home-page "https://github.com/vtraag/louvain-igraph") (synopsis "Algorithm for methods of community detection in large networks") (description @@ -366,9 +409,9 @@ install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib) "/test")) #t))))) (inputs - `(("openblas" ,openblas))) + (list openblas)) (native-inputs - `(("googletest" ,googletest))) + (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 @@ -418,8 +461,7 @@ CPUFLAGS = ~{~a ~}~%" ("python*" ,python) ("swig" ,swig))) (propagated-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy))) + (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."))) @@ -436,13 +478,22 @@ Faiss library."))) (base32 "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1")))) (build-system python-build-system) - (arguments '(#:tests? #f)) ; tests are not included + (arguments + '(#:tests? #f ;tests are not included + #:phases (modify-phases %standard-phases + (add-after 'unpack 'fix-requirements + (lambda _ + (substitute* "setup.py" + (("python-igraph >=") + "igraph >="))))))) (native-inputs - `(("pkg-config" ,pkg-config))) + ;; XXX: setuptools >= 58 as shipped with Python 3.9+ removes support + ;; for lib2to3, so use this older variant. + (list pkg-config python-setuptools)) (inputs - `(("igraph" ,igraph))) + (list igraph)) (propagated-inputs - `(("python-igraph" ,python-igraph))) + (list python-igraph)) (home-page "https://github.com/vtraag/leidenalg") (synopsis "Community detection in large networks") (description @@ -472,9 +523,7 @@ of the Louvain algorithm, for a number of different methods.") "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (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 @@ -498,9 +547,9 @@ isolating planarity obstructions.") "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("igraph" ,igraph))) + (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 @@ -521,9 +570,9 @@ of graphs.") "08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("gd" ,gd))) + (list 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 @@ -550,36 +599,28 @@ transformed into common image formats for display or printing.") "0v58in4rwk9fhjarjw6xfxpx5zz2z13sy3yvd14b5kr0884yw6sz")))) (build-system gnu-build-system) (arguments - `(#:configure-flags + `(#: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=" - (assoc-ref %outputs "out") - "/lib/python" - ,(version-major+minor - (package-version - (car (assoc-ref - (package-inputs this-package) - "python")))) - "/site-packages/")))) + (site-packages %build-inputs %outputs))))) (native-inputs - `(("gcc-10" ,gcc-10) - ("ncurses" ,ncurses) - ("pkg-config" ,pkg-config))) + (list ncurses pkg-config)) (inputs - `(("boost" ,boost) - ("cairomm" ,cairomm) - ("cgal" ,cgal) - ("expat" ,expat) - ("gmp" ,gmp) - ("gtk+" ,gtk+) - ("python" ,python-wrapper) - ("sparsehash" ,sparsehash))) + (list boost + cairomm-1.14 + cgal + expat + gmp + gtk+ + python-wrapper + sparsehash)) (propagated-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pycairo" ,python-pycairo) - ("python-scipy" ,python-scipy))) + (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 |