diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 181 |
1 files changed, 159 insertions, 22 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 8ebf3d27b1..58d127277c 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -20,6 +20,8 @@ ;;; Copyright © 2022 Paul A. Patience <paul@apatience.com> ;;; Copyright © 2022 Wiktor Żelazny <wzelazny@vurv.cz> ;;; Copyright © 2022 Eric Bavier <bavier@posteo.net> +;;; Copyright © 2022 Antero Mejr <antero@mailbox.org> +;;; Copyright © 2022 jgart <jgart@dismail.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -48,6 +50,7 @@ #:use-module (gnu packages crypto) #:use-module (gnu packages databases) #:use-module (gnu packages gcc) + #:use-module (gnu packages image) #:use-module (gnu packages image-processing) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) @@ -289,26 +292,6 @@ logic, also known as grey logic.") genetic variation data.") (license license:expat))) -(define-public python-sgp4 - (package - (name "python-sgp4") - (version "2.12") - (source - (origin - (method url-fetch) - (uri (pypi-uri "sgp4" version)) - (sha256 - (base32 "0dncp9i5b6afkg7f8mj9j0qzsp008b8v73yc0qkmizhpns7mvwvx")))) - (build-system python-build-system) - (propagated-inputs - (list python-numpy)) - (home-page "https://github.com/brandon-rhodes/python-sgp4") - (synopsis "Track earth satellite TLE orbits using SGP4") - (description - "This package provides a Python implementation of the most recent version -of the SGP4 satellite tracking algorithm.") - (license license:expat))) - (define-public python-trimesh (package (name "python-trimesh") @@ -347,6 +330,26 @@ manipulation and analysis, in the style of the Polygon object in the Shapely library.") (license license:expat))) +(define-public python-tspex + (package + (name "python-tspex") + (version "0.6.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "tspex" version)) + (sha256 + (base32 + "0x64ki1nzhms2nb8xpng92bzh5chs850dvapr93pkg05rk22m6mv")))) + (build-system python-build-system) + (propagated-inputs + (list python-matplotlib python-numpy python-pandas python-xlrd)) + (home-page "https://apcamargo.github.io/tspex/") + (synopsis "Calculate tissue-specificity metrics for gene expression") + (description + "This package provides a Python package for calculating +tissue-specificity metrics for gene expression.") + (license license:gpl3+))) + (define-public python-pandas (package (name "python-pandas") @@ -500,6 +503,47 @@ annotated with a few interface descriptions and turns it into a native Python module with the same interface, but (hopefully) faster.") (license license:bsd-3))) +(define-public python-pyts + (package + (name "python-pyts") + (version "0.12.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyts" version)) + (sha256 + (base32 + "1cb5jwp8g52a3hxay6mxbfzk16ly6yj6rphq8cwbwk1k2jdf11dg")))) + (build-system python-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-v" + ;; XXX: This test fails for unknown reasons + ;; Expected: + ;; (40, 9086) + ;; Got: + ;; (40, 9088) + "-k" + "not pyts.multivariate.transformation.weasel_muse.WEASELMUSE"))))))) + (propagated-inputs + (list python-joblib + python-matplotlib + python-numba + python-numpy + python-scikit-learn + python-scipy)) + (native-inputs + (list python-pytest python-pytest-cov)) + (home-page "https://github.com/johannfaouzi/pyts") + (synopsis "Python package for time series classification") + (description + "This package provides a Python package for time series classification.") + (license license:bsd-3))) + (define-public python-bottleneck (package (name "python-bottleneck") @@ -631,14 +675,14 @@ and visualization with these data structures.") (define-public python-msgpack-numpy (package (name "python-msgpack-numpy") - (version "0.4.6.post0") + (version "0.4.8") (source (origin (method url-fetch) (uri (pypi-uri "msgpack-numpy" version)) (sha256 (base32 - "0syzy645mwcy7lfjwz6pc8f9p2vv1qk4limc8iina3l5nnf0rjyz")))) + "0sbfanbkfs6c77np4vz0ayrwnv99bpn5xgj5fnf2yhhk0lcd6ry6")))) (build-system python-build-system) (propagated-inputs (list python-msgpack python-numpy)) @@ -1290,6 +1334,26 @@ powerful visualization backend to facilitate rapid prototyping, analysis, and visual integration of spatially referenced datasets.") (license license:expat))) +(define-public python-simplespectral + (package + (name "python-simplespectral") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "SimpleSpectral" version)) + (sha256 + (base32 "0qh3xwdv9cwcqdamvglrhm586p4yaq1hd291py1fvykhk2a2d4w6")))) + (build-system python-build-system) + (propagated-inputs + (list python-numpy python-scipy)) + (home-page "https://github.com/xmikos/simplespectral") + (synopsis "FFT module for Python") + (description + "This package provides a simplified @code{scipy.signal.spectral} module +to do spectral analysis in Python.") + (license license:expat))) + (define-public python-traittypes (package (name "python-traittypes") @@ -1426,6 +1490,55 @@ Python, from the Sheffield machine learning group. GPy implements a range of machine learning algorithms based on GPs.") (license license:bsd-3))) +(define-public python-pydicom + (package + (name "python-pydicom") + (version "2.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pydicom/pydicom") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18l26s53yf5j9yh2zwq83n74qq4f2iq0cfblamsw4y9k35l1c108")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (chdir "pydicom/tests") + (invoke "python3" "-m" "pytest" "-k" ;skip tests using web data + (string-append + "not test_jpeg_ls_pixel_data.py" + " and not test_gdcm_pixel_data.py" + " and not test_pillow_pixel_data.py" + " and not test_rle_pixel_data.py" + " and not Test_JPEG_LS_Lossless_transfer_syntax" + " and not test_numpy_pixel_data.py" + " and not test_data_manager.py" + " and not test_handler_util.py" + " and not test_overlay_np.py" + " and not test_encoders_pydicom.py" + " and not test_encaps.py" + " and not test_reading_ds_with_known_tags_with_UN_VR" + " and not TestDatasetOverlayArray" + " and not TestReader" + " and not test_filewriter.py")))))))) + (native-inputs (list python-pytest)) + (inputs (list gdcm libjpeg-turbo)) + (propagated-inputs (list python-numpy python-pillow)) + (home-page "https://github.com/pydicom/pydicom") + (synopsis "Python library for reading and writing DICOM data") + (description "@code{python-pydicom} is a Python library for reading and +writing DICOM medical imaging data. It lets developers read, modify and write +DICOM data in a pythonic way.") + (license license:expat))) + (define-public python-deepdish (package (name "python-deepdish") @@ -1462,6 +1575,30 @@ of use as pickling or @code{numpy.save}, but with the language interoperability offered by HDF5.") (license license:bsd-3))) +(define-public python-simple-pid + (package + (name "python-simple-pid") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "simple-pid" version)) + (sha256 + (base32 + "094mz6rmfq1h0gpns5vlxb7xf9297hlkhndw7g9k95ziqfkv7mk0")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "unittest" "discover" "tests/"))))))) + (home-page "https://github.com/m-lundberg/simple-pid") + (synopsis "Easy to use PID controller") + (description "This package provides a simple and easy-to-use @acronym{PID, +proportional-integral-derivative} controller.") + (license license:expat))) + (define-public python-opt-einsum (package (name "python-opt-einsum") |