diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 134 |
1 files changed, 92 insertions, 42 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 1cd430de5f..37d4ef78ad 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2017, 2020 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> @@ -16,7 +16,7 @@ ;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net> ;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com> ;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego@posteo.net> -;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -45,7 +45,6 @@ #:use-module (guix build-system ocaml) #:use-module (guix build-system pyproject) #:use-module (guix build-system python) - #:use-module (guix build-system r) #:use-module (guix build-system trivial) #:use-module (guix git-download) #:use-module (gnu packages) @@ -298,36 +297,19 @@ training, HMM clustering, HMM mixtures.") (define-public guile-aiscm (package (name "guile-aiscm") - (version "0.24.2") + (version "0.25.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/wedesoft/aiscm") - (commit "2e16e38391bf1638f1dd9a1cf4b25a25f6626078"))) + (commit "v0.25.2"))) (file-name (git-file-name name version)) (sha256 (base32 - "1gwqpzl6irpaszkpxaf5wliwq19280632hlgxs3ikjkfg8mkqql0")))) + "1sagpxwrqxkn5b9zqzd07c9r7swmw45q672pa8fy6s71iw6a0x77")))) (build-system gnu-build-system) (arguments (list - #:configure-flags - #~(list (string-append "OPENCV_CFLAGS=-I" #$(this-package-input "opencv") - "/include/opencv4") - (let ((modules - (list "aruco" "barcode" "bgsegm" "bioinspired" - "calib3d" "ccalib" "core" "datasets" "dnn" - "dnn_objdetect" "dnn_superres" "dpm" "face" - "features2d" "flann" "freetype" "fuzzy" "hdf" - "hfs" "highgui" "img_hash" "imgcodecs" "imgproc" - "intensity_transform" "line_descriptor" "mcc" - "ml" "objdetect" "optflow" "phase_unwrapping" - "photo" "plot" "quality" "rapid" "reg" "rgbd" - "saliency" "shape" "stereo" "stitching" - "structured_light" "superres" "surface_matching" - "text" "tracking" "video" "videoio" "videostab" - "wechat_qrcode" "ximgproc" "xobjdetect" "xphoto"))) - (format #false "OPENCV_LIBS=~{-lopencv_~a~^ ~}" modules))) #:make-flags #~(list (string-append "GUILE_CACHE=" #$output "/lib/guile/3.0/site-ccache") (string-append "GUILE_EXT=" #$output "/lib/guile/3.0/extensions") @@ -396,13 +378,12 @@ training, HMM clustering, HMM mixtures.") libxv mesa mjpegtools - opencv pandoc pulseaudio tensorflow)) (native-inputs - (list clang-11 - llvm-11 + (list clang-13 + llvm-13 pkg-config protobuf-c-for-aiscm autoconf @@ -438,7 +419,7 @@ Performance is achieved by using the LLVM JIT compiler.") "CFLAGS=-fcommon"))) (inputs (list perl)) - (home-page "http://micans.org/mcl/") + (home-page "https://micans.org/mcl/") (synopsis "Clustering algorithm for graphs") (description "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a @@ -565,7 +546,7 @@ sample proximities between pairs of cases.") "0hlbdmjjf1jgsvi3d2hwni5lz3l9a5bzj6ijpbawa8a7cbrpp66y")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--enable-ngram-fsts"))) - (home-page "http://www.openfst.org") + (home-page "https://www.openfst.org") (synopsis "Library for weighted finite-state transducers") (description "OpenFst is a library for constructing, combining, optimizing, and searching weighted finite-state transducers (FSTs).") @@ -906,7 +887,7 @@ with a single function call.") (invoke "ctest")))))) (native-inputs (list catch-framework)) - (home-page "http://reactivex.io/") + (home-page "https://reactivex.io/") (synopsis "Reactive Extensions for C++") (description "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for @@ -3371,27 +3352,26 @@ Python.") (define-public python-hmmlearn (package (name "python-hmmlearn") - (version "0.2.7") + (version "0.2.8") (source (origin (method url-fetch) (uri (pypi-uri "hmmlearn" version)) (sha256 (base32 - "1qgnf1kdxicygy8nvpv866iqvwq0rc6xkd3s6slmvxvsy8h2fjvb")))) + "1yd5l9ra37mks41mn5bigav7xpb161a9yqlcnz4ir076vkik2sb9")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (with-directory-excursion (string-append (assoc-ref outputs "out") "/lib") - (invoke "python" "-m" "pytest")))))))) + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion (string-append #$output "/lib") + (invoke "python" "-m" "pytest")))))))) (propagated-inputs (list pybind11 - python-cython python-numpy python-scikit-learn python-scipy @@ -3409,7 +3389,7 @@ of Hidden Markov Models.") (define-public liblantern (package (name "liblantern") - (version "0.9.0") + (version "0.9.1") (source (origin (method git-fetch) @@ -3418,7 +3398,7 @@ of Hidden Markov Models.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0bjd0ym547k46ci8xnwsry7x8w5k65cl86snlcrfn4vs3fald2y9")))) + (base32 "1rycs7fgm03fxp8lxj8ljrdwy5whxd4554xzklbcmn4mcwbxgg57")))) (build-system cmake-build-system) (arguments (list @@ -3818,3 +3798,73 @@ fi" original-exe original-exe))) (chmod exe #o555))))))) + +(define-public python-brian2 + (package + (name "python-brian2") + (version "2.5.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "Brian2" version)) + (sha256 + (base32 + "1g48hzn3cdsvfjgz64s3kvh5d5287ggjxdyacb7wh2n5nd5iqlf7")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") + ;; Must be run in a different directory, otherwise compiled + ;; modules are not found. + (with-directory-excursion "/tmp" + ;; Invoking brian2.test() is preferred to running pytest. + (invoke "python" "-c" + "import brian2, sys; sys.exit(0 if brian2.test() else 1)")))))))) + (propagated-inputs (list python-cython ; Required by codegen. + python-jinja2 + python-numpy + python-py-cpuinfo + python-pyparsing + ;; Required by codegen. + python-setuptools + python-sympy)) + (native-inputs (list python-pytest python-pytest-xdist)) + (home-page "https://briansimulator.org/") + (synopsis "Clock-driven simulator for spiking neural networks") + (description + "Brian is a simulator for spiking neural networks written in Python. It +is therefore designed to be easy to learn and use, highly flexible and +easily extensible.") + (license license:cecill))) + +(define-public python-brian2tools + (package + (name "python-brian2tools") + (version "0.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "brian2tools" version)) + (sha256 + (base32 + "0fn028mfy3qlzjkadd0wr5d7rcplijd5jphln414xifvvsb9jcc2")))) + (build-system python-build-system) + ;; Both pypi tarball and git repo lack test files. + (arguments (list #:tests? #f)) + (propagated-inputs (list python-brian2 + python-libneuroml + python-markdown-strings + python-matplotlib + python-pylems + python-setuptools + python-setuptools-scm)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/brian-team/brian2tools") + (synopsis "Tools for the Brian 2 simulator") + (description "Visualization and NeuroML import/export tools for the +Brian 2 simulator.") + (license license:cecill))) + |