;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019, 2021 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>
(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
("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.
(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
(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"))
(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
(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
(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")))
(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,
(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
(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
HCoop / jackhill / guix / guix.git / blobdiff