diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 323 |
1 files changed, 169 insertions, 154 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 8df3178bd8..d43c5227ff 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -152,7 +152,7 @@ (define-public dlpack (package (name "dlpack") - (version "1.0") + (version "1.1") (source (origin (method git-fetch) @@ -161,10 +161,10 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "169slm88jin4ddhdwk1qhqzzkhkwk1jrz35i7abhcqkry9wjib4f")))) + (base32 "0vlp8gcf7s3snalj6xmvgqxxn96fki6gw9hzph30gmgdbaz730j6")))) (build-system cmake-build-system) (arguments (list #:tests? #f)) ;No tests. - (home-page "https://github.com/dmlc/dlpack") + (home-page "https://dmlc.github.io/dlpack/latest/") (synopsis "In memory tensor structure") (description "DLPack is an in-memory tensor structure for sharing tensors among @@ -221,7 +221,7 @@ family of functions.") (define-public python-faster-whisper (package (name "python-faster-whisper") - (version "1.1.1") + (version "1.2.0") (source (origin (method git-fetch) @@ -230,7 +230,7 @@ family of functions.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0g9cdvphifn4rqhh7p4z1d3pp6bhcx0jmcahjigvcgry0qsijgfn")))) + (base32 "0wmc9aszpnbr60l5v97np0rc3zsz4pldjald7kmnr668rhpakzcj")))) (build-system pyproject-build-system) ;; XXX: Currently tests requires model download, which we'd rather avoid ;; in Guix unless we're sure about the FOSS weights. To test in source : @@ -302,30 +302,41 @@ distributions.") (license license:asl2.0))) (define-public fann - ;; The last release is >100 commits behind, so we package from git. - (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7")) + ;; The last release is 14 years old. + (let ((commit "1783cbf6239a597c4d29f694e227e22b8d4f4bf6") + (revision "2")) (package (name "fann") - (version (string-append "2.2.0-1." (string-take commit 8))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/libfann/fann") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x")))) + (version (git-version "2.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/libfann/fann") + (commit commit))) + (modules '((guix build utils))) + (snippet #~(delete-file-recursively "lib/googletest")) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0jlcxl0czlr3982mak3935mb08i2f368f0jsxca91ppgfd596ldr")))) (build-system cmake-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out"))) - (with-directory-excursion (string-append (getcwd) "/tests") - (invoke "./fann_tests")))))))) - (home-page "http://leenissen.dk/fann/wp/") + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-googletest + (lambda _ + (substitute* "CMakeLists.txt" + (("ADD_SUBDIRECTORY\\( lib/googletest \\)") + "")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "tests" + (invoke "./fann_tests")))))))) + (native-inputs (list googletest)) + (home-page "https://leenissen.dk/") (synopsis "Fast Artificial Neural Network") (description "FANN is a neural network library, which implements multilayer @@ -336,39 +347,40 @@ sparsely connected networks.") (define-public libsvm (package (name "libsvm") - (version "3.23") + (version "336") (source (origin - (method url-fetch) - (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/" - name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/cjlin1/libsvm/") + (commit (string-append "v" version)))) (sha256 - (base32 "0jpaq0rr92x38p4nk3gjan79ip67m6p80anb28z1d8601miysyi5")))) + (base32 "03ns6frhfdcyl661ws1yqbzsa6m8wrmba544vlacghry2kg88hn2")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; no "check" target - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'build 'build-lib - (lambda _ - (invoke "make" "lib"))) - (replace 'install ; no ‘install’ target - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin/")) - (lib (string-append out "/lib/")) - (inc (string-append out "/include/libsvm"))) - (mkdir-p bin) - (for-each (lambda (file) - (copy-file file (string-append bin file))) - '("svm-train" - "svm-predict" - "svm-scale")) - (mkdir-p lib) - (install-file "libsvm.so.2" lib) - (mkdir-p inc) - (install-file "svm.h" inc))))))) + (list + #:tests? #f ;no "check" target + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-after 'build 'build-lib + (lambda _ + (invoke "make" "lib"))) + (replace 'install + ;no "install" target + (lambda _ + (for-each (lambda (file) + (install-file file + (string-append #$output "/bin"))) + '("svm-train" "svm-predict" "svm-scale")) + (install-file "libsvm.so.4" + (string-append #$output "/lib")) + (symlink (string-append #$output "/lib/libsvm.so.4") + (string-append #$output "/lib/libsvm.so")) + (install-file "svm.h" + (string-append #$output "/include/" + #$name))))))) + (native-inputs (list python-minimal-wrapper)) (home-page "https://www.csie.ntu.edu.tw/~cjlin/libsvm/") (synopsis "Library for Support Vector Machines") (description @@ -427,35 +439,20 @@ machine learning algorithms based on GPs.") (license license:bsd-3))) (define-public python-libsvm - (package (inherit libsvm) + (package + (inherit libsvm) (name "python-libsvm") - (build-system gnu-build-system) + (build-system pyproject-build-system) (arguments - `(#:tests? #f ; no "check" target - #:make-flags '("-C" "python") - #:phases - (modify-phases %standard-phases - (delete 'configure) - (replace - 'install ; no ‘install’ target - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((site (string-append (assoc-ref outputs "out") - "/lib/python" - (string-take - (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages/"))) - (substitute* "python/svm.py" - (("../libsvm.so.2") "libsvm.so.2")) - (mkdir-p site) - (for-each (lambda (file) - (copy-file file (string-append site (basename file)))) - (find-files "python" "\\.py")) - (copy-file "libsvm.so.2" - (string-append site "libsvm.so.2"))) - #t))))) - (inputs - (list python)) + (list + #:tests? #f ;no "check" target + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'chdir + (lambda _ + (chdir "python")))))) + (native-inputs (list python-setuptools python-wheel)) + (propagated-inputs (list libsvm python-scipy)) (synopsis "Python bindings of libSVM"))) (define-public python-mcfit @@ -979,16 +976,17 @@ algorithm.") (define-public openmm (package (name "openmm") - (version "8.1.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/openmm/openmm") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "064vv6zaci30pj38z5lwfqscxssm67jqxkz30hcya9vm4ng831d5")))) + (version "8.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openmm/openmm") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0pcy1f6r4h6z0b75gx4lcnkf7yr8342w2dch7jml1ycmzpqkxvfx")))) (build-system cmake-build-system) (arguments (list @@ -1141,16 +1139,17 @@ optimizing, and searching weighted finite-state transducers (FSTs).") (define-public sentencepiece (package (name "sentencepiece") - (version "0.1.97") + (version "0.2.1") (source (origin (method git-fetch) - (uri (git-reference - (url "https://github.com/google/sentencepiece") - (commit (string-append "v" version)))) + (uri + (git-reference + (url "https://github.com/google/sentencepiece/") + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1kzfkp2pk0vabyw3wmkh16h11chzq63mzc20ddhsag5fp6s91ajg")))) + (base32 "1yzsaam3kk9fqzxfc3nm2pskwq1bdgkrijmcmzmg5x0338rn0hmb")))) (build-system cmake-build-system) (arguments (list #:tests? #f)) ;no tests (native-inputs (list gperftools)) @@ -1194,23 +1193,24 @@ cardinality matching from a bipartite graph.") (define-public python-persim (package (name "python-persim") - (version "0.3.2") + (version "0.3.8") (source (origin (method url-fetch) (uri (pypi-uri "persim" version)) (sha256 - (base32 "0q8wfakx8q4h3ryvw8cba0v6z7xn9139qkrzs3mi1ggyzacnx9d7")))) + (base32 "03d4kgakpgj54c3pl9dkqrkbmj6w13gmczkds5jagf3n85c1hgg1")))) (build-system pyproject-build-system) - (propagated-inputs (list python-deprecated - python-hopcroftkarp - python-joblib - python-matplotlib - python-numpy - python-scikit-learn - python-scipy)) - (native-inputs (list python-pytest python-pytest-cov python-setuptools - python-wheel)) + (native-inputs + (list python-pytest python-setuptools-next)) + (propagated-inputs + (list python-deprecated + python-hopcroftkarp + python-joblib + python-matplotlib + python-numpy + python-scikit-learn + python-scipy)) (home-page "https://persim.scikit-tda.org") (synopsis "Tools for analyzing persistence diagrams in Python") (description @@ -1456,22 +1456,21 @@ storing tensors safely.") (define-public python-sentencepiece (package + (inherit sentencepiece) (name "python-sentencepiece") - (version "0.1.97") - (source - (origin - (method url-fetch) - (uri (pypi-uri "sentencepiece" version)) - (sha256 - (base32 "0v0z9ryl66432zajp099bcbnwkkldzlpjvgnjv9bq2vi19g300f9")))) (build-system python-build-system) - (native-inputs (list pkg-config)) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "python")))))) + (native-inputs (list pkg-config protobuf)) (propagated-inputs (list sentencepiece)) - (home-page "https://github.com/google/sentencepiece") (synopsis "SentencePiece python wrapper") (description "This package provides a Python wrapper for the SentencePiece -unsupervised text tokenizer.") - (license license:asl2.0))) +unsupervised text tokenizer."))) (define-public python-sentence-transformers (package @@ -3892,7 +3891,6 @@ advanced research.") (build-system cmake-build-system) (arguments (list - #:tests? #false ;tests are not building now #:build-type "Release" #:modules '((ice-9 match) (guix build utils) @@ -3908,6 +3906,7 @@ advanced research.") "-DTFLITE_ENABLE_GPU=ON" "-DTFLITE_ENABLE_RUY=ON" + "-DTFLITE_ENABLE_XNNPACK=ON" ;; TODO: turn on Farmhash ;;"-DSYSTEM_FARMHASH=ON" @@ -3925,11 +3924,6 @@ advanced research.") (string-append "-Druy_DIR=" #$(this-package-input "ruy") "/lib/cmake/ruy") - ;; TODO: The build system attempts to build xnnpack from source. We - ;; would like to use our xnnpack package here, but this requires more - ;; work. - "-DTFLITE_ENABLE_XNNPACK=OFF" - ;; Don't fetch the sources. We have these already "-Dgemmlowp_POPULATED=TRUE" "-Degl_headers_POPULATED=TRUE" @@ -3941,6 +3935,7 @@ advanced research.") "-Dgoogle_benchmark_POPULATED=TRUE" "-Dnsync_POPULATED=TRUE" "-Dre2_POPULATED=TRUE" + "-Dxnnpack_POPULATED=TRUE" "-DFFT2D_SOURCE_DIR=/tmp/fft2d" "-DFARMHASH_SOURCE_DIR=/tmp/farmhash" @@ -3975,6 +3970,21 @@ advanced research.") (with-directory-excursion "/tmp/fft2d" (invoke "tar" "--strip-components=1" "-xf" (assoc-ref inputs "fft2d-src"))))) + (add-after 'copy-sources 'opencl-fix + (lambda _ (substitute* "delegates/gpu/cl/opencl_wrapper.h" + (("cl_ndrange_kernel_command_properties_khr") + "cl_command_properties_khr")))) + (add-after 'opencl-fix 'absl-fix + (lambda _ (substitute* '( + "delegates/gpu/cl/cl_operation.h" + "delegates/gpu/common/task/qcom_thin_filter_desc.cc" + "delegates/gpu/common/tasks/special/thin_pointwise_fuser.cc") + (("#include <vector>") + "#include <vector>\n\n#include \"absl/strings/str_cat.h\"\n")))) + (add-after 'opencl-fix 'stdint-fix + (lambda _ (substitute* "kernels/internal/spectrogram.cc" + (("#include <math.h>") + "#include <math.h>\n#include <cstdint>\n")))) (add-after 'build 'build-shared-library (lambda* (#:key configure-flags #:allow-other-keys) (mkdir-p "c") @@ -3999,7 +4009,7 @@ advanced research.") (when tests? (invoke "ctest" "-L" "plain"))))))) (inputs - `(("abseil-cpp" ,abseil-cpp-20200923.3) + `(("abseil-cpp" ,abseil-cpp) ("cpuinfo" ,cpuinfo) ("eigen" ,eigen) ("fp16" ,fp16) @@ -4015,7 +4025,7 @@ advanced research.") ("python" ,python) ("ruy" ,ruy) ("re2" ,re2) - ;;("xnnpack" ,xnnpack) ; TODO: use Guix's copy of xnnpack + ("xnnpack" ,xnnpack) ("vulkan-headers" ,vulkan-headers))) (native-inputs `(("pkg-config" ,pkg-config) @@ -4064,11 +4074,10 @@ devices.") (base32 "1x4ad1jhn84fywlk031fmv1kxyiscclmrqn9hhj8gz0mh7z9vcrh")))) (build-system cmake-build-system) (arguments - `(#:configure-flags - (list "-DGOOGLE_TEST=ON"))) + (list + #:configure-flags #~(list "-DGOOGLE_TEST=ON"))) (native-inputs - `(("googletest" ,googletest) - ("python" ,python-wrapper))) + (list googletest python-wrapper)) (home-page "https://github.com/dmlc/dmlc-core") (synopsis "Common bricks library for machine learning") (description @@ -4297,7 +4306,7 @@ methodxs at scale on CPU or GPU.") (define-public python-umap-learn (package (name "python-umap-learn") - (version "0.5.8") + (version "0.5.9") (source (origin (method git-fetch) ;no tests in pypi release @@ -4306,7 +4315,7 @@ methodxs at scale on CPU or GPU.") (commit (string-append "release-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0pdlb6qn9vnvabksiabxmcj30j8ff7526mz1qszrbdl5kh2sl7sm")))) + (base32 "0pkniia9lccdbshwl4sh2iria7dny13qk0flkk67msb777sm5bmn")))) (build-system pyproject-build-system) (arguments (list @@ -5596,24 +5605,23 @@ as torchvision, torchtext, and others.") (define-public python-readchar (package (name "python-readchar") - (version "4.0.5") - (source (origin - (method url-fetch) - (uri (pypi-uri "readchar" version)) - (sha256 - (base32 - "09n8vl2jjbnbnrzfvkynijrnwrqvc91bb2267zg8r261sz15d908")))) + (version "4.2.1") + (source + (origin + ;; There is no tests data in PyPI archive. + (method git-fetch) + (uri (git-reference + (url "https://github.com/magmax/python-readchar/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16ypci664l54ka6ickwkpaa2id14h9h00y7z24z0bv0szld4mrxg")))) (build-system pyproject-build-system) - (arguments - (list - #:phases - '(modify-phases %standard-phases - ;; This one file requires the msvcrt module, which we don't have. - (add-after 'unpack 'delete-windows-file - (lambda _ - (delete-file "readchar/_win_read.py")))))) - (propagated-inputs (list python-setuptools)) - (native-inputs (list python-wheel)) + (native-inputs + (list python-pytest + python-pytest-cov + python-setuptools-next)) (home-page "https://github.com/magmax/python-readchar") (synopsis "Library to easily read single chars and key strokes") (description "This package provides a Python library to easily read single @@ -6423,7 +6431,7 @@ linear algebra routines needed for structured matrices (or operators).") (define-public python-botorch (package (name "python-botorch") - (version "0.14.0") + (version "0.15.1") (source (origin (method git-fetch) ;no tests in PyPI (uri (git-reference @@ -6432,10 +6440,17 @@ linear algebra routines needed for structured matrices (or operators).") (file-name (git-file-name name version)) (sha256 (base32 - "1hgjjzdqcs8y0z20vkdzzpbm0nvnxmrav4mfvbpp0gny8pk64913")))) + "1c6p5h5gypiyj59820q2w3k7rx715r3vxxcr5mnwdjbhi4l2q47a")))) (build-system pyproject-build-system) (arguments - (list #:test-flags #~(list "-k" "not test_all_cases_covered") + ;; 7 failed, 1502 passed, 1 skipped, 1 deselected, 807 warnings + (list #:test-flags #~(list "-k" + (string-append + "not test_all_cases_covered" + " and not test_input_constructors" + " and not test_gen" + " and not test_mock" + " and not test_evaluation")) #:phases #~(modify-phases %standard-phases (add-before 'build 'pretend-version @@ -6582,8 +6597,8 @@ simple speech recognition.") "lib."))))))))) (define-public nerd-dictation - (let* ((commit "0eb44b7fd0927d69c92de5566e5807ed2c2e20b7") - (revision "1")) + (let* ((commit "03ce043a6d569a5bb9a715be6a8e45d8ba0930fd") + (revision "2")) (package (name "nerd-dictation") (version (git-version "0" revision commit)) @@ -6595,7 +6610,7 @@ simple speech recognition.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0frdpswv6w3cwj3c7wd5w8gj3s1hvpdwd48qhfhfxf7imahz9bqf")))) + (base32 "0ksnlpy2jcldxamq7bsbcgxgafcmgxkbjccd4fwmmn0y814kkz9k")))) (build-system pyproject-build-system) (arguments (list |