diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 253 |
1 files changed, 184 insertions, 69 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index fbc06f96b6..75cc100851 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -43,6 +43,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #: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) @@ -1180,6 +1181,52 @@ number of threads used in the threadpool-backed of common native libraries used for scientific computing and data science (e.g. BLAS and OpenMP).") (license license:bsd-3))) +(define-public python-imbalanced-learn + (package + (name "python-imbalanced-learn") + (version "0.9.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "imbalanced-learn" version)) + (sha256 + (base32 + "0qnrmysnqpc8ii1w5n8mci20gcjhmjr7khvk7f2apdbqc2pgf52f")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'unbreak-tests + (lambda _ + ;; The doctests require tensorflow + (substitute* "setup.cfg" + (("--doctest-modules") "")) + ;; Some tests require a home directory + (setenv "HOME" (getcwd)) + ;; We don't have keras + (delete-file "imblearn/keras/tests/test_generator.py") + ;; We don't have tensorflow + (delete-file "imblearn/tensorflow/tests/test_generator.py")))))) + (propagated-inputs + (list python-joblib + python-numpy + python-scikit-learn + python-scipy + python-threadpoolctl)) + (native-inputs + (list python-black + python-flake8 + python-mypy + python-pandas + python-pytest + python-pytest-cov)) + (home-page "https://github.com/scikit-learn-contrib/imbalanced-learn") + (synopsis "Toolbox for imbalanced dataset in machine learning") + (description "This is a Python package offering a number of re-sampling +techniques commonly used in datasets showing strong between-class imbalance. +It is compatible with @code{scikit-learn}.") + (license license:expat))) + (define-public python-pynndescent (package (name "python-pynndescent") @@ -1283,6 +1330,76 @@ good at identifying feature interactions that are normally overlooked by standard feature selection algorithms.") (license license:expat))) +(define-public python-cleanlab + (package + (name "python-cleanlab") + (version "2.2.0") + ;; The version on pypi does not come with tests. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cleanlab/cleanlab") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00dqhxpwg781skknw943ynll2s44g4j125dx8aapk1d5d71sbzqy")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'disable-bad-tests + (lambda _ + ;; XXX This requires pytest lazy_fixture + (delete-file "tests/test_multilabel_classification.py") + ;; Requires tensorflow + (delete-file "tests/test_frameworks.py") + ;; Tries to download datasets from the internet at runtime. + (delete-file "tests/test_dataset.py")))))) + (propagated-inputs + (list python-numpy + python-pandas + python-scikit-learn + python-termcolor + python-tqdm)) + (native-inputs + (list python-pytest + python-pytorch + python-torchvision)) + (home-page "https://cleanlab.ai") + (synopsis "Automatically find and fix dataset issues") + (description + "cleanlab automatically finds and fixes errors in any ML dataset. This +data-centric AI package facilitates machine learning with messy, real-world +data by providing clean labels during training.") + (license license:agpl3+))) + +(define-public python-cleanlab-1 + (package + (inherit python-cleanlab) + (name "python-cleanlab") + (version "1.0.1") + ;; The version on pypi does not come with tests. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cleanlab/cleanlab") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03kw2agnhadmrq9zvrlvvlc2c37dpflga5nhmsaag8scw223gqyp")))) + (build-system pyproject-build-system) + (arguments (list)) + (propagated-inputs + (list python-numpy + python-scikit-learn + python-scipy + python-tqdm)) + (native-inputs + (list python-pytest)))) + (define-public python-cmaes (package (name "python-cmaes") @@ -1435,35 +1552,39 @@ interactive learning.") (define-public python-hyperopt (package (name "python-hyperopt") - (version "0.2.5") + (version "0.2.7") (source (origin (method url-fetch) (uri (pypi-uri "hyperopt" version)) (sha256 - (base32 "1k4ma8ci0bxghw7g4ms944zak1pi83yv2d6bxd7fcslm1zalfq5w")))) - (build-system python-build-system) + (base32 "0jd1ghmm423kbhjvd6pxq92y5vkz25390687fcnd7fshh3jrmy0v")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (lambda* (#:key tests? #:allow-other-keys) (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest" "--ignore" + (invoke "python" "-m" "pytest" ;; Needs python-pyspark. - "hyperopt/tests/test_spark.py" + "--ignore" "hyperopt/tests/integration/test_spark.py" ;; Needs both python-scikit-learn and python-lightgbm. - "--ignore" "hyperopt/tests/test_atpe_basic.py" + "--ignore" "hyperopt/tests/unit/test_atpe_basic.py" ;; The tests below need python-lightgbm. - "-k" (string-append "not test_branin" - " and not test_distractor" - " and not test_q1lognormal" - " and not test_quadratic1" - " and not test_twoarms")))))))) + "-k" + (string-append "not test_branin" + " and not test_distractor" + " and not test_q1lognormal" + " and not test_quadratic1" + " and not test_twoarms" + ;; XXX Type error with this version of scipy + " and not test_distribution_rvs")))))))) (propagated-inputs (list python-cloudpickle python-future + python-py4j python-networkx python-numpy python-scipy @@ -1471,8 +1592,6 @@ interactive learning.") python-tqdm)) (native-inputs (list python-black - python-ipython - python-ipyparallel python-nose python-pymongo python-pytest)) @@ -1485,8 +1604,8 @@ discrete, and conditional dimensions.") ;; There have been no proper releases yet. (define-public kaldi - (let ((commit "dd107fd594ac58af962031c1689abfdc10f84452") - (revision "0") + (let ((commit "be22248e3a166d9ec52c78dac945f471e7c3a8aa") + (revision "1") (openfst openfst-1.7.3)) ;; Temporary bypass for upstream issues (package (name "kaldi") @@ -1499,14 +1618,14 @@ discrete, and conditional dimensions.") (file-name (git-file-name name version)) (sha256 (base32 - "0iqbzgn7gzmgwvjfzifpbwwidxx887qmlgmsjkg7b1yzyfv00l21")))) + "1wkxz3p0h68mxbg41i1wygir2r4rraxbb4672xkkvvs85r6c8r8i")))) (build-system gnu-build-system) (arguments `(#:test-target "test" #:phases (modify-phases %standard-phases (add-after 'unpack 'chdir - (lambda _ (chdir "src") #t)) + (lambda _ (chdir "src"))) (replace 'configure (lambda* (#:key build system inputs outputs #:allow-other-keys) (when (not (or (string-prefix? "x86_64" system) @@ -1552,8 +1671,7 @@ discrete, and conditional dimensions.") (invoke "make" "-C" "onlinebin" "depend") (invoke "make" "-C" "onlinebin") (invoke "make" "-C" "gst-plugin" "depend") - (invoke "make" "-C" "gst-plugin") - #t)) + (invoke "make" "-C" "gst-plugin"))) ;; TODO: also install the executables. (replace 'install (lambda* (#:key outputs #:allow-other-keys) @@ -1574,8 +1692,7 @@ discrete, and conditional dimensions.") (install-file file target-dir))) (find-files "." "\\.h")) (install-file "gst-plugin/libgstonlinegmmdecodefaster.so" - (string-append lib "/gstreamer-1.0")) - #t)))))) + (string-append lib "/gstreamer-1.0")))))))) (inputs (list alsa-lib `(,gfortran "lib") @@ -1697,8 +1814,8 @@ written in C++.") (find-files "." "\\.h"))))))))))) (define-public gst-kaldi-nnet2-online - (let ((commit "cb227ef43b66a9835c14eb0ad39e08ee03c210ad") - (revision "2")) + (let ((commit "7888ae562a65bd7e406783ce2c33535bc66a30ef") + (revision "3")) (package (name "gst-kaldi-nnet2-online") (version (git-version "0" revision commit)) @@ -1710,12 +1827,13 @@ written in C++.") (file-name (git-file-name name version)) (sha256 (base32 - "1i6ffwiavxx07ri0lxix6s8q0r31x7i4xxvhys5jxkixf5q34w8g")))) + "0xp59a6lmx1y24i8bkmxcm27lhm5x5m6y41670yjzhamcbnx8jcr")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; there are none - #:make-flags - (list (string-append "SHELL=" + (list + #:tests? #f ; there are none + #:make-flags + '(list (string-append "SHELL=" (assoc-ref %build-inputs "bash") "/bin/bash") (string-append "KALDI_ROOT=" (assoc-ref %build-inputs "kaldi-src")) @@ -1723,33 +1841,32 @@ written in C++.") (assoc-ref %build-inputs "kaldi") "/lib") "KALDI_FLAVOR=dynamic") #:phases - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ (chdir "src") #t)) - (replace 'configure - (lambda* (#:key inputs #:allow-other-keys) - (let ((glib (assoc-ref inputs "glib"))) - (setenv "CXXFLAGS" "-fPIC") - (setenv "CPLUS_INCLUDE_PATH" - (string-append glib "/include/glib-2.0:" - glib "/lib/glib-2.0/include:" - (assoc-ref inputs "gstreamer") - "/include/gstreamer-1.0"))) - (substitute* "Makefile" - (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "") - (("\\$\\(error Cannot find") "#")) - #t)) - (add-before 'build 'build-depend - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "depend" make-flags))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib/gstreamer-1.0"))) - (install-file "libgstkaldinnet2onlinedecoder.so" lib) - #t)))))) + '(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (replace 'configure + (lambda* (#:key inputs #:allow-other-keys) + (let ((glib (assoc-ref inputs "glib"))) + (setenv "CXXFLAGS" "-fPIC") + (setenv "CPLUS_INCLUDE_PATH" + (string-append glib "/include/glib-2.0:" + glib "/lib/glib-2.0/include:" + (assoc-ref inputs "gstreamer") + "/include/gstreamer-1.0:" + (getenv "CPLUS_INCLUDE_PATH")))) + (substitute* "Makefile" + (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "") + (("\\$\\(error Cannot find") "#")))) + (add-before 'build 'build-depend + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "depend" make-flags))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib/gstreamer-1.0"))) + (install-file "libgstkaldinnet2onlinedecoder.so" lib))))))) (inputs - (list glib gstreamer jansson openfst kaldi)) + (list glib gstreamer jansson openfst-1.7.3 kaldi)) (native-inputs `(("bash" ,bash) ("glib:bin" ,glib "bin") ; glib-genmarshal @@ -1765,8 +1882,8 @@ automatically.") (define-public kaldi-gstreamer-server ;; This is the tip of the py3 branch - (let ((commit "f68cab490be7eb0da2af1475fbc16655f50a60cb") - (revision "2")) + (let ((commit "f79e204d751a5964918001822e4520fa2acfd246") + (revision "3")) (package (name "kaldi-gstreamer-server") (version (git-version "0" revision commit)) @@ -1778,7 +1895,7 @@ automatically.") (file-name (git-file-name name version)) (sha256 (base32 - "17lh1368vkg8ngrcbn2phvigzlmalrqg6djx2gg61qq1a0nj87dm")))) + "1iijq8jmgdxr7961inal1ggs496ymxradm51m4sqx8vl983x14y8")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are no tests that can be run automatically @@ -1808,8 +1925,7 @@ automatically.") "-m" "compileall" "-f" ; force rebuild ,file))) - (find-files "." "\\.py$"))) - #t)) + (find-files "." "\\.py$"))))) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -1848,14 +1964,13 @@ exec ~a ~a/~a \"$@\"~%" (list server client worker) (list "master_server.py" "client.py" - "worker.py"))) - #t)))))) + "worker.py"))))))))) (inputs - `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online) - ("python" ,python-wrapper) - ("python-pygobject" ,python-pygobject) - ("python-pyyaml" ,python-pyyaml) - ("python-tornado" ,python-tornado-6))) + (list gst-kaldi-nnet2-online + python-wrapper + python-pygobject + python-pyyaml + python-tornado-6)) (home-page "https://github.com/alumae/kaldi-gstreamer-server") (synopsis "Real-time full-duplex speech recognition server") (description "This is a real-time full-duplex speech recognition server, |