;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix svn-download)
+ #:use-module (guix build-system asdf)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system ocaml)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages image)
#:use-module (gnu packages linux)
+ #:use-module (gnu packages lisp-xyz)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages ocaml)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages serialization)
(home-page "http://leenissen.dk/fann/wp/")
(synopsis "Fast Artificial Neural Network")
(description
- "FANN is a free open source neural network library, which implements
-multilayer artificial neural networks in C with support for both fully
-connected and sparsely connected networks.")
+ "FANN is a neural network library, which implements multilayer
+artificial neural networks in C with support for both fully connected and
+sparsely connected networks.")
(license license:lgpl2.1))))
(define-public libsvm
(uri (svn-reference
(url "http://svn.code.sf.net/p/ghmm/code/trunk")
(revision svn-revision)))
- (file-name (string-append name "-" version))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
(string-append indent
"@unittest.skip(\"Disabled by Guix\")\n"
line)))
- #t))
- (add-after 'disable-broken-tests 'autogen
- (lambda _
- (invoke "bash" "autogen.sh"))))))
+ #t)))))
(inputs
`(("python" ,python-2) ; only Python 2 is supported
("libxml2" ,libxml2)))
(inputs
`(("giflib" ,giflib)
("lapack" ,lapack)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("libx11" ,libx11)
("openblas" ,openblas)
(define-public python-scikit-learn
(package
(name "python-scikit-learn")
- (version "0.20.3")
+ (version "0.20.4")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "08aaby5zphfxy83mggg35bwyka7wk91l2qijh8kk0bl08dikq8dl"))))
+ "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj"))))
(build-system python-build-system)
(arguments
`(#:phases
(setenv "HOME" "/tmp")
(invoke "pytest" "sklearn" "-m" "not network")))
- ;; FIXME: This fails with permission denied
- (delete 'reset-gzip-timestamps))))
+ (add-before 'reset-gzip-timestamps 'make-files-writable
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Make sure .gz files are writable so that the
+ ;; 'reset-gzip-timestamps' phase can do its work.
+ (let ((out (assoc-ref outputs "out")))
+ (for-each make-file-writable
+ (find-files out "\\.gz$"))
+ #t))))))
(inputs
`(("openblas" ,openblas)))
(native-inputs
("openssl" ,openssl)
("zlib" ,zlib)))
(native-inputs
- `(("protobuf" ,protobuf-next)
+ `(("protobuf" ,protobuf)
("python" ,python-wrapper)))
(home-page "https://grpc.io")
(synopsis "High performance universal RPC framework")
- (description "gRPC is a modern open source high performance @dfn{Remote
-Procedure Call} (RPC) framework that can run in any environment. It can
-efficiently connect services in and across data centers with pluggable support
-for load balancing, tracing, health checking and authentication. It is also
-applicable in last mile of distributed computing to connect devices, mobile
-applications and browsers to backend services.")
+ (description "gRPC is a modern high performance @dfn{Remote Procedure Call}
+(RPC) framework that can run in any environment. It can efficiently connect
+services in and across data centers with pluggable support for load balancing,
+tracing, health checking and authentication. It is also applicable in last
+mile of distributed computing to connect devices, mobile applications and
+browsers to backend services.")
(license license:asl2.0)))
;; Note that Tensorflow includes a "third_party" directory, which seems to not
#t))))))
(native-inputs
`(("pkg-config" ,pkg-config)
- ("protobuf:native" ,protobuf-next) ; protoc
- ("protobuf:src" ,(package-source protobuf-next))
+ ("protobuf:native" ,protobuf-3.6) ; protoc
+ ("protobuf:src" ,(package-source protobuf-3.6))
("eigen:src" ,(package-source eigen-for-tensorflow))
+ ;; install_pip_packages.sh wants setuptools 39.1.0 specifically.
+ ("python-setuptools" ,python-setuptools-for-tensorflow)
+
;; The commit hashes and URLs for third-party source code are taken
;; from "tensorflow/workspace.bzl".
("boringssl-src"
("python-gast" ,python-gast)
("python-grpcio" ,python-grpcio)
("python-numpy" ,python-numpy)
- ("python-protobuf" ,python-protobuf-next)
+ ("python-protobuf" ,python-protobuf-3.6)
("python-six" ,python-six)
("python-termcolo" ,python-termcolor)
("python-wheel" ,python-wheel)))
("eigen" ,eigen-for-tensorflow)
("gemmlowp" ,gemmlowp-for-tensorflow)
("lmdb" ,lmdb)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("giflib" ,giflib)
("grpc" ,grpc)
("jsoncpp" ,jsoncpp-for-tensorflow)
("snappy" ,snappy)
("sqlite" ,sqlite)
- ("protobuf" ,protobuf-next)
+ ("protobuf" ,protobuf-3.6)
("python" ,python-wrapper)
("zlib" ,zlib)))
(home-page "https://tensorflow.org")
(origin
(method url-fetch)
(uri (pypi-uri "Keras" version))
+ (patches (search-patches "python-keras-integration-test.patch"))
(sha256
(base32
"1j8bsqzh49vjdxy6l1k4iwax5vpjzniynyd041xjavdzvfii1dlh"))))
@item Runs seamlessly on CPU and GPU.
@end itemize\n")
(license license:expat)))
+
+(define-public sbcl-cl-libsvm-format
+ (let ((commit "3300f84fd8d9f5beafc114f543f9d83417c742fb")
+ (revision "0"))
+ (package
+ (name "sbcl-cl-libsvm-format")
+ (version (git-version "0.1.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/masatoi/cl-libsvm-format.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0284aj84xszhkhlivaigf9qj855fxad3mzmv3zfr0qzb5k0nzwrg"))))
+ (build-system asdf-build-system/sbcl)
+ (native-inputs
+ `(("prove" ,sbcl-prove)
+ ("prove-asdf" ,sbcl-prove-asdf)))
+ (inputs
+ `(("alexandria" ,sbcl-alexandria)))
+ (synopsis "LibSVM data format reader for Common Lisp")
+ (description
+ "This Common Lisp library provides a fast reader for data in LibSVM
+format.")
+ (home-page "https://github.com/masatoi/cl-libsvm-format")
+ (license license:expat))))
+
+(define-public cl-libsvm-format
+ (sbcl-package->cl-source-package sbcl-cl-libsvm-format))
+
+(define-public ecl-cl-libsvm-format
+ (sbcl-package->ecl-package sbcl-cl-libsvm-format))
+
+(define-public sbcl-cl-online-learning
+ (let ((commit "fc7a34f4f161cd1c7dd747d2ed8f698947781423")
+ (revision "0"))
+ (package
+ (name "sbcl-cl-online-learning")
+ (version (git-version "0.5" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/masatoi/cl-online-learning.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "14x95rlg80ay5hv645ki57pqvy12v28hz4k1w0f6bsfi2rmpxchq"))))
+ (build-system asdf-build-system/sbcl)
+ (native-inputs
+ `(("prove" ,sbcl-prove)
+ ("prove-asdf" ,sbcl-prove-asdf)))
+ (inputs
+ `(("cl-libsvm-format" ,sbcl-cl-libsvm-format)
+ ("cl-store" ,sbcl-cl-store)))
+ (arguments
+ `(;; FIXME: Tests pass but then the check phase crashes
+ #:tests? #f))
+ (synopsis "Online Machine Learning for Common Lisp")
+ (description
+ "This library contains a collection of machine learning algorithms for
+online linear classification written in Common Lisp.")
+ (home-page "https://github.com/masatoi/cl-online-learning")
+ (license license:expat))))
+
+(define-public cl-online-learning
+ (sbcl-package->cl-source-package sbcl-cl-online-learning))
+
+(define-public ecl-cl-online-learning
+ (sbcl-package->ecl-package sbcl-cl-online-learning))
+
+(define-public sbcl-cl-random-forest
+ (let ((commit "85fbdd4596d40e824f70f1b7cf239cf544e49d51")
+ (revision "0"))
+ (package
+ (name "sbcl-cl-random-forest")
+ (version (git-version "0.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/masatoi/cl-random-forest.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "097xv60i1ndz68sg9p4pc7c5gvyp9i1xgw966b4wwfq3x6hbz421"))))
+ (build-system asdf-build-system/sbcl)
+ (native-inputs
+ `(("prove" ,sbcl-prove)
+ ("prove-asdf" ,sbcl-prove-asdf)
+ ("trivial-garbage" ,sbcl-trivial-garbage)))
+ (inputs
+ `(("alexandria" ,sbcl-alexandria)
+ ("cl-libsvm-format" ,sbcl-cl-libsvm-format)
+ ("cl-online-learning" ,sbcl-cl-online-learning)
+ ("lparallel" ,sbcl-lparallel)))
+ (arguments
+ `(;; The tests download data from the Internet
+ #:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'add-sb-cltl2-dependency
+ (lambda _
+ ;; sb-cltl2 is required by lparallel when using sbcl, but it is
+ ;; not loaded automatically.
+ (substitute* "cl-random-forest.asd"
+ (("\\(in-package :cl-user\\)")
+ "(in-package :cl-user) #+sbcl (require :sb-cltl2)"))
+ #t)))))
+ (synopsis "Random Forest and Global Refinement for Common Lisp")
+ (description
+ "CL-random-forest is an implementation of Random Forest for multiclass
+classification and univariate regression written in Common Lisp. It also
+includes an implementation of Global Refinement of Random Forest.")
+ (home-page "https://github.com/masatoi/cl-random-forest")
+ (license license:expat))))
+
+(define-public cl-random-forest
+ (sbcl-package->cl-source-package sbcl-cl-random-forest))
+
+(define-public ecl-cl-random-forest
+ (sbcl-package->ecl-package sbcl-cl-random-forest))
+
+(define-public gloo
+ (let ((version "0.0.0") ; no proper version tag
+ (commit "ca528e32fea9ca8f2b16053cff17160290fc84ce")
+ (revision "0"))
+ (package
+ (name "gloo")
+ (version (git-version version revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/facebookincubator/gloo.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1q9f80zy75f6njrzrqkmhc0g3qxs4gskr7ns2jdqanxa2ww7a99w"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("googletest" ,googletest)))
+ (arguments
+ `(#:configure-flags '("-DBUILD_TEST=1")
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "make" "gloo_test")
+ #t)))))
+ (synopsis "Collective communications library")
+ (description
+ "Gloo is a collective communications library. It comes with a
+number of collective algorithms useful for machine learning applications.
+These include a barrier, broadcast, and allreduce.")
+ (home-page "https://github.com/facebookincubator/gloo")
+ (license license:bsd-3))))
+
+(define-public python-umap-learn
+ (package
+ (name "python-umap-learn")
+ (version "0.3.10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "umap-learn" version))
+ (sha256
+ (base32
+ "02ada2yy6km6zgk2836kg1c97yrcpalvan34p8c57446finnpki1"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-nose" ,python-nose)))
+ (propagated-inputs
+ `(("python-numba" ,python-numba)
+ ("python-numpy" ,python-numpy)
+ ("python-scikit-learn" ,python-scikit-learn)
+ ("python-scipy" ,python-scipy)))
+ (home-page "https://github.com/lmcinnes/umap")
+ (synopsis
+ "Uniform Manifold Approximation and Projection")
+ (description
+ "Uniform Manifold Approximation and Projection is a dimension reduction
+technique that can be used for visualisation similarly to t-SNE, but also for
+general non-linear dimension reduction.")
+ (license license:bsd-3)))
HCoop / jackhill / guix / guix.git / blobdiff