diff options
Diffstat (limited to 'gnu/packages/graph.scm')
| -rw-r--r-- | gnu/packages/graph.scm | 103 |
1 files changed, 98 insertions, 5 deletions
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 26b9d03a73..e3aa6ba478 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2017-2024 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, 2021, 2022, 2024 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> @@ -57,6 +57,8 @@ #:use-module (gnu packages graphics) #:use-module (gnu packages graphviz) #:use-module (gnu packages gtk) + #:use-module (gnu packages linux) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) @@ -64,6 +66,7 @@ #:use-module (gnu packages pretty-print) #:use-module (gnu packages python) #:use-module (gnu packages python-build) + #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) @@ -279,7 +282,7 @@ lines.") (define-public python-plotly (package (name "python-plotly") - (version "5.14.1") + (version "5.20.0") (source (origin (method git-fetch) (uri (git-reference @@ -288,7 +291,7 @@ lines.") (file-name (git-file-name name version)) (sha256 (base32 - "12iy5cswn5c0590fvl87nr6vfyhvbxymrldh4c7dfm2gn6h8z8w0")))) + "0i22sv8p3kl84nkldbv1253kld85rbwp2pdxivxn64wwflfpqvx6")))) (build-system python-build-system) (arguments (list @@ -426,6 +429,57 @@ algorithm for community detection in large networks.") large networks.") (license license:gpl3+))) +(define-public python-graphtools + (package + (name "python-graphtools") + (version "1.5.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KrishnaswamyLab/graphtools") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1aaxhij4y5z2vvc34qnb5py6nw3ciz35a3z4lfr223f9kvfpqgak")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Incompatibility with sklearn. + ;; 'kNNLandmarkGraph' object has no attribute '_landmark_op' + (delete-file "test/test_landmark.py") + (setenv "LOKY_MAX_CPU_COUNT" "1") + (invoke "nose2" "-v"))))))) + (propagated-inputs + (list python-deprecated + python-future + python-numpy + python-pygsp + python-scikit-learn + python-scipy + python-tasklogger)) + (native-inputs + (list util-linux ;for lscpu + python-anndata + python-black + python-coverage + python-coveralls + python-nose + python-nose2 + python-pandas + python-parameterized + python-igraph)) + (home-page "https://github.com/KrishnaswamyLab/graphtools") + (synopsis "Tools for building and manipulating graphs in Python") + (description "This package provides tools for building and manipulating +graphs in Python.") + (license license:gpl3))) + (define-public python-louvain-igraph (package (name "python-louvain-igraph") @@ -468,6 +522,43 @@ millions of nodes (as long as they can fit in memory). The core function is algorithm for a number of different methods.") (license license:gpl3+))) +(define-public python-pygsp + (package + (name "python-pygsp") + (version "0.5.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "PyGSP" version)) + (sha256 + (base32 "002q4z3p3ka81rzhgi66qqmz1ccrg9hwch4bax7jsqixg64asx28")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; These all fail due to a type error in scipy. + '(list "-k" (string-append "not test_bunny" + " and not test_lowstretchtree" + " and not test_nngraph" + " and not test_plot_graphs" + " and not test_randomregular")) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'disable-doctests + (lambda _ + (substitute* "pygsp/tests/test_all.py" + (("def test_docstrings.*") "def _disabled_test_docstrings():\n") + (("return doctest.DocFileSuite.*") "return False\n") + (("suites.append\\(test_docstrings.*") + ""))))))) + (propagated-inputs (list python-numpy python-scikit-image python-scipy)) + (native-inputs (list python-coverage python-coveralls python-flake8)) + (home-page "https://github.com/epfl-lts2/pygsp") + (synopsis "Graph Signal Processing in Python") + (description "The PyGSP is a Python package to ease signal processing on +graphs.") + (license license:bsd-3))) + (define-public faiss (package (name "faiss") @@ -727,7 +818,7 @@ transformed into common image formats for display or printing.") (define-public python-graph-tool (package (name "python-graph-tool") - (version "2.57") + (version "2.59") (source (origin (method url-fetch) (uri (string-append @@ -735,13 +826,15 @@ transformed into common image formats for display or printing.") version ".tar.bz2")) (sha256 (base32 - "0wmvzx509lvigja6cfxh45r4b7wns64vmik0x4rz4y4fnxrhw2m2")))) + "1bmck5fcihj9lr5kd8x624bdi9xhfc13pl4mwzv74jr5lz07kr6d")))) (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))) + ;; The build process peaks around 4GB/RAM per core. + #:parallel-build? #f #:configure-flags (list (string-append "--with-boost=" (assoc-ref %build-inputs "boost")) |