diff options
Diffstat (limited to 'gnu/packages/graph.scm')
| -rw-r--r-- | gnu/packages/graph.scm | 145 |
1 files changed, 102 insertions, 43 deletions
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 084fdf8c90..de68ff78b1 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -8,6 +8,8 @@ ;;; Copyright © 2020 Pierre Langlois <[email protected]> ;;; Copyright © 2021 Vinicius Monego <[email protected]> ;;; Copyright © 2021 Alexandre Hannud Abdo <[email protected]> +;;; Copyright © 2021, 2022 Maxim Cournoyer <[email protected]> +;;; Copyright © 2022 Marius Bakke <[email protected]> ;;; ;;; 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) @@ -60,31 +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 - (list gmp + (list arpack-ng + gmp glpk libxml2 lapack openblas - zlib)) + plfit + suitesparse)) (home-page "https://igraph.org") (synopsis "Network analysis and visualization") (description @@ -95,36 +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 (list igraph)) (propagated-inputs (list python-texttable)) (native-inputs - (list pkg-config 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 @@ -181,14 +236,7 @@ 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 (list python-ipywidgets python-pytest python-xarray)) (propagated-inputs @@ -204,7 +252,7 @@ lines.") (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 @@ -239,6 +287,8 @@ 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 (list python-networkx python-numpy)) (home-page "https://github.com/taynaud/python-louvain") @@ -428,9 +478,18 @@ 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 - (list 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 (list igraph)) (propagated-inputs |