diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 206 |
1 files changed, 159 insertions, 47 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 7a9605bb3b..c10e5c4a55 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -151,6 +151,42 @@ representations and sentence classification.") (inputs (list fasttext)) (native-inputs (list pybind11)))) +(define-public python-funsor + (package + (name "python-funsor") + (version "0.4.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "funsor" version)) + (sha256 + (base32 "0cgysij0dix0fikyz2x4f8jvaskm5s5a04s07chzaz2dw1fpxdq8")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-makefun python-multipledispatch + python-numpy python-opt-einsum + python-typing-extensions)) + (native-inputs (list python-black + python-flake8 + python-isort + python-nbsphinx + python-pandas + python-pillow + python-pyro-api + python-pytest + python-pytest-xdist + python-requests + python-scipy + python-sphinx + python-sphinx-gallery + python-sphinx-rtd-theme + python-torchvision)) + (home-page "https://github.com/pyro-ppl/funsor") + (synopsis "Tensor-like library for functions and distributions") + (description + "This package provides a tensor-like library for functions and +distributions.") + (license license:asl2.0))) + (define-public fann ;; The last release is >100 commits behind, so we package from git. (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7")) @@ -260,6 +296,42 @@ classification.") (list python)) (synopsis "Python bindings of libSVM"))) +(define-public python-ml-collections + (package + (name "python-ml-collections") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ml_collections" version)) + (sha256 + (base32 "1k38psfzqsqnl99fl578bd07zdmvfkja61r3sgjs2fj3xircrvrz")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; TODO: we can't seem to run the config_flags tests, because + ;; the installed Python files conflict with those from the + ;; source directory, resulting in constants to be defined more + ;; than once. + (invoke "pytest" "ml_collections/config_dict/tests" + ;; This one fails because we're testing the __main__ + ;; class, not config_dict_test. + "-k" "not testJSONConversionBestEffort"))))))) + (propagated-inputs + (list python-absl-py python-contextlib2 python-pyyaml python-six)) + (native-inputs (list python-mock python-pytest)) + (home-page "https://github.com/google/ml_collections") + (synopsis "Python collections designed for Machine Learning usecases") + (description + "ML Collections is a library of Python collections designed for Machine +Learning usecases.") + (license license:asl2.0))) + (define-public ghmm ;; The latest release candidate is several years and a couple of fixes have ;; been published since. This is why we download the sources from the SVN @@ -1460,6 +1532,54 @@ computing environments.") data analysis.") (license license:bsd-3))) +(define-public python-scikit-learn-extra + (package + (name "python-scikit-learn-extra") + (version "0.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/scikit-learn-contrib/scikit-learn-extra") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0yy6ka94ss88f3r7b6mpjf1l8lnv7aabhsg844pigfj8lfiv0wvl")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'build 'build-ext + (lambda _ + (invoke "python" "setup.py" "build_ext" + "--inplace"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Restrict OpenBLAS threads to prevent segfaults while testing! + (setenv "OPENBLAS_NUM_THREADS" "1") + + ;; Some tests require write access to $HOME. + (setenv "HOME" "/tmp") + + ;; Step out of the source directory to avoid interference; + ;; we want to run the installed code with extensions etc. + (with-directory-excursion "/tmp" + (invoke "pytest" "-vv" "--pyargs" + "sklearn_extra" + ;; ignore tests that require network + "-k" "not test_build")))))))) + (propagated-inputs (list python-numpy python-scikit-learn python-scipy)) + (native-inputs (list python-pytest python-pytest-cov python-cython)) + (home-page "https://github.com/scikit-learn-contrib/scikit-learn-extra") + (synopsis "Set of tools for scikit-learn") + (description + "This package provides a Python module for machine learning that extends +scikit-learn. It includes algorithms that are useful but do not satisfy the +scikit-learn inclusion criteria, for instance due to their novelty or lower +citation number.") + (license license:bsd-3))) + (define-public python-thinc (package (name "python-thinc") @@ -1591,45 +1711,42 @@ and forecasting.") (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")))) + (version "0.11.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "imbalanced-learn" version)) + (sha256 + (base32 "1p4gdgc8nsq0vjmw4y4d2bp9g0m1c23d0zgrzs90pnz6b24ax0km")))) (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)) + #:test-flags '(list "-k" + ;; Although we cannot satify the Tensorflow and Keras requirements + ;; (python-keras >= 2.4.3 and tensorflow >= 2.4.3), all tests + ;; besides these pass. + "not balanced_batch_generator and not BalancedBatchGenerator") + #:phases '(modify-phases %standard-phases + (add-after 'unpack 'unbreak-tests + (lambda _ + ;; Some tests require a home directory + (setenv "HOME" + (getcwd))))))) + (propagated-inputs (list python-joblib python-numpy python-scikit-learn + python-scipy python-threadpoolctl)) + (native-inputs (list python-black + python-flake8 + python-keras + python-mypy + python-numpydoc + python-pandas + python-pytest + python-pytest-cov + tensorflow)) (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 + (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))) @@ -1672,7 +1789,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.") (define-public python-opentsne (package (name "python-opentsne") - (version "0.7.1") + (version "1.0.0") (source (origin (method git-fetch) ; no tests in PyPI release @@ -1681,7 +1798,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "12wp98mh67v6v683yi7wbv8zhpafrfz21z349bww4wgi2q7bl3il")))) + (base32 "05qzpq1zjs42bl0z8girfwcj3nfxs1a99c5525vp3589sglk351g")))) (build-system python-build-system) (arguments `(#:phases @@ -1851,9 +1968,9 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.") (license license:expat))) (define-public python-autograd - (let* ((commit "442205dfefe407beffb33550846434baa90c4de7") + (let* ((commit "c6d81ce7eede6db801d4e9a92b27ec5d409d0eab") (revision "0") - (version (git-version "0.0.0" revision commit))) + (version (git-version "1.5" revision commit))) (package (name "python-autograd") (home-page "https://github.com/HIPS/autograd") @@ -1864,19 +1981,14 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.") (commit commit))) (sha256 (base32 - "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4")) + "04kljgydng42xlg044h6nbzxpban1ivd6jzb8ydkngfq88ppipfk")) (file-name (git-file-name name version)))) (version version) - (build-system python-build-system) + (build-system pyproject-build-system) (native-inputs (list python-nose python-pytest)) (propagated-inputs (list python-future python-numpy)) - (arguments - `(#:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "py.test" "-v")))))) (synopsis "Efficiently computes derivatives of NumPy code") (description "Autograd can automatically differentiate native Python and NumPy code. It can handle a large subset of Python's features, including loops, @@ -2030,13 +2142,13 @@ discrete, and conditional dimensions.") (define-public python-deepxde (package (name "python-deepxde") - (version "1.9.3") + (version "1.10.0") (source (origin (method url-fetch) (uri (pypi-uri "DeepXDE" version)) (sha256 (base32 - "1zw2gqssc0s3maf4gdjckxmzx1d3036hbp1iir26kd08hxj93vzs")))) + "0fdxrjrm7l19yx6n8vaklxlhwzx0bw9n08vp8idikzdifybz5gij")))) (build-system pyproject-build-system) (arguments (list #:tests? #f ; there are no tests |