X-Git-Url: https://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/6e31d6f3c478144de1ad185dc7341d5513f464c0..e0f983c0d55e301fc646d956039cc425ad18076d:/gnu/packages/graph.scm?ds=sidebyside diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 762ee30632..d2e4c875a1 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice -;;; Copyright © 2019 Efraim Flashner +;;; Copyright © 2019, 2021 Efraim Flashner ;;; Copyright © 2019 Andreas Enge ;;; Copyright © 2020 Alexander Krotov ;;; Copyright © 2020 Pierre Langlois @@ -57,18 +57,19 @@ (define-public igraph (package (name "igraph") - (version "0.8.1") + (version "0.8.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/igraph/igraph/releases/" "download/" version "/igraph-" version ".tar.gz")) (sha256 - (base32 "0wbvrac3ip3lqmbkckhnxa2swlbc86l1h8mazdlb618kx3winvi6")))) + (base32 "127q6q40kbmvd62yhbz6dlfk370qiq98s1iscyagpgbpjwb4xvyf")))) (build-system gnu-build-system) (arguments `(#:configure-flags - (list "--with-external-glpk" + (list "--disable-static" + "--with-external-glpk" "--with-external-blas" "--with-external-lapack"))) (inputs @@ -78,7 +79,7 @@ ("lapack" ,lapack) ("openblas" ,openblas) ("zlib" ,zlib))) - (home-page "http://igraph.org") + (home-page "https://igraph.org") (synopsis "Network analysis and visualization") (description "This package provides a library for the analysis of networks and graphs. @@ -90,14 +91,13 @@ more.") (define-public python-igraph (package (inherit igraph) (name "python-igraph") - (version "0.8.0") + (version "0.8.2") (source (origin (method url-fetch) (uri (pypi-uri "python-igraph" version)) (sha256 - (base32 - "13mbrlmnbgbzw6y8ws7wj0a3ly3in8j4l1ngi6yxvgvxxi4bprj7")))) + (base32 "0wkxrs28qdvnrz7d4jzcf2bh6v2yqzx3wyfziihfgsi2gn6n60a6")))) (build-system python-build-system) (arguments '(#:configure-flags @@ -122,91 +122,6 @@ more.") (home-page "https://pypi.org/project/python-igraph/") (synopsis "Python bindings for the igraph network analysis library"))) -(define-public r-igraph - (package - (name "r-igraph") - (version "1.2.5") - (source - (origin - (method url-fetch) - (uri (cran-uri "igraph" version)) - (sha256 - (base32 - "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c")))) - (build-system r-build-system) - (native-inputs - `(("gfortran" ,gfortran))) - (inputs - `(("gmp" ,gmp) - ("glpk" ,glpk) - ("libxml2" ,libxml2) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-pkgconfig" ,r-pkgconfig))) - (home-page "http://igraph.org") - (synopsis "Network analysis and visualization") - (description - "This package provides routines for simple graphs and network analysis. -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 r-diffusionmap - (package - (name "r-diffusionmap") - (version "1.2.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "diffusionMap" version)) - (sha256 - (base32 - "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j")))) - (properties `((upstream-name . "diffusionMap"))) - (build-system r-build-system) - (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-scatterplot3d" ,r-scatterplot3d))) - (home-page "https://www.r-project.org") - (synopsis "Diffusion map") - (description "This package implements the diffusion map method of data -parametrization, including creation and visualization of diffusion maps, -clustering with diffusion K-means and regression using the adaptive regression -model.") - (license license:gpl2))) - -(define-public r-rgraphviz - (package - (name "r-rgraphviz") - (version "2.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Rgraphviz" version)) - (sha256 - (base32 - "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y")))) - (properties `((upstream-name . "Rgraphviz"))) - (build-system r-build-system) - ;; FIXME: Rgraphviz bundles the sources of an older variant of - ;; graphviz. It does not build with the latest version of graphviz, so - ;; we do not add graphviz to the inputs. - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-graph" ,r-graph))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (home-page "https://bioconductor.org/packages/Rgraphviz") - (synopsis "Plotting capabilities for R graph objects") - (description - "This package interfaces R with the graphviz library for plotting R graph -objects from the @code{graph} package.") - (license license:epl1.0))) - (define-public r-rbiofabric (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac") (revision "1")) @@ -216,7 +131,7 @@ objects from the @code{graph} package.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/wjrl/RBioFabric.git") + (url "https://github.com/wjrl/RBioFabric") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -236,16 +151,16 @@ lines.") (define-public python-plotly (package (name "python-plotly") - (version "4.8.1") + (version "4.14.3") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/plotly/plotly.py.git") + (url "https://github.com/plotly/plotly.py") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz")))) + "02wlgy7gf3v5ckiq9ab3prm53cckxkavlghqgkk9xw2sfmmrn61q")))) (build-system python-build-system) (arguments `(#:phases @@ -255,12 +170,14 @@ lines.") (chdir "packages/python/plotly") #t)) (replace 'check - (lambda _ - (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"))) + (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")) + #t)) (add-before 'reset-gzip-timestamps 'make-files-writable (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -268,16 +185,17 @@ lines.") (find-files out "\\.gz")) #t)))))) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("python-ipywidgets" ,python-ipywidgets) + ("python-pytest" ,python-pytest) + ("python-xarray" ,python-xarray))) (propagated-inputs - `(("python-decorator" ,python-decorator) - ("python-ipywidgets" ,python-ipywidgets) + `(("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) - ("python-xarray" ,python-xarray))) + ("python-statsmodels" ,python-statsmodels))) (home-page "https://plotly.com/python/") (synopsis "Interactive plotting library for Python") (description "Plotly's Python graphing library makes interactive, @@ -318,7 +236,7 @@ subplots, multiple-axes, polar charts, and bubble charts. ") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/vtraag/louvain-igraph.git") + (url "https://github.com/vtraag/louvain-igraph") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -351,7 +269,7 @@ not be used for new projects.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/facebookresearch/faiss.git") + (url "https://github.com/facebookresearch/faiss") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256