From 05c13b3149ecba94da30b4cac743f0c770171cf1 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 28 Sep 2022 09:49:52 +0200 Subject: gnu: Add python-simplespectral. * gnu/packages/python-science.scm (python-simplespectral): New variable. --- gnu/packages/python-science.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 30b75ca7f3..f2cbfb0043 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1290,6 +1290,26 @@ (define-public python-pyvista 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") -- cgit v1.2.3 From 70cac2829fe180099c3ea7637053ff8bf1cc1760 Mon Sep 17 00:00:00 2001 From: jgart Date: Fri, 7 Oct 2022 16:59:11 -0500 Subject: gnu: Add python-simple-pid. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-science.scm (python-simple-pid): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/python-science.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 8e38e69d97..94a4c922a5 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -20,6 +20,7 @@ ;;; Copyright © 2022 Paul A. Patience ;;; Copyright © 2022 Wiktor Żelazny ;;; Copyright © 2022 Eric Bavier +;;; Copyright © 2022 jgart ;;; ;;; This file is part of GNU Guix. ;;; @@ -1482,6 +1483,30 @@ (define-public python-deepdish 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") -- cgit v1.2.3 From b19c12c2d7d274bcebc5195e22ccf7721391519e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Nov 2022 18:29:21 +0100 Subject: gnu: Add python-pyts. * gnu/packages/python-science.scm (python-pyts): New variable. --- gnu/packages/python-science.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 94a4c922a5..b389a27a9a 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -501,6 +501,47 @@ (define-public python-pythran 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") -- cgit v1.2.3 From ba8679fb2452f4466a98a99edf050ea7452c83f4 Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Fri, 11 Nov 2022 11:55:32 +0100 Subject: gnu: Add python-tspex. * gnu/packages/python-science.scm (python-tspex): New variable. Co-authored-by: Ricardo Wurmus --- gnu/packages/python-science.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index b389a27a9a..52fe1460bb 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -348,6 +348,26 @@ (define-public python-trimesh 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") -- cgit v1.2.3 From 9ddc4e5b0338accbc707992050d2a9c21c41e05e Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Fri, 2 Dec 2022 14:09:43 +0100 Subject: gnu: python-msgpack-numpy: Update to 0.4.8. * gnu/packages/python-science.scm (python-msgpack-numpy): Update to 0.4.8. --- gnu/packages/python-science.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 52fe1460bb..ba99b57bcb 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -693,14 +693,14 @@ (define-public python-xarray (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)) -- cgit v1.2.3 From 6468d9c131921c82a4389f0c1670807fb635f4f2 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 28 Nov 2022 23:27:17 +0000 Subject: gnu: python-sgp4: Update to 2.21. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The latest version passes build on aarch64-linux system. * gnu/packages/python-science.scm (python-sgp4): Update to 2.21. Signed-off-by: Ludovic Courtès --- gnu/packages/python-science.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index ba99b57bcb..ef4d93500a 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -293,13 +293,13 @@ (define-public python-scikit-allel (define-public python-sgp4 (package (name "python-sgp4") - (version "2.12") + (version "2.21") (source (origin (method url-fetch) (uri (pypi-uri "sgp4" version)) (sha256 - (base32 "0dncp9i5b6afkg7f8mj9j0qzsp008b8v73yc0qkmizhpns7mvwvx")))) + (base32 "1vzcrlrlzmhbycdz16m8v241l8zx49vsy81wcd0yjxs80isvhyb1")))) (build-system python-build-system) (propagated-inputs (list python-numpy)) -- cgit v1.2.3 From 7f380a2e26f59ef99b4a02d65c67192a9ad24cb5 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 28 Nov 2022 23:27:18 +0000 Subject: gnu: python-sgp4: Move to astronomy. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/astronomy.scm: (python-sgp4): Move here from python-science.scm. [description]: Expand description, annotate acronyms, add link to CelesTrak. Signed-off-by: Ludovic Courtès --- gnu/packages/astronomy.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/python-science.scm | 20 -------------------- 2 files changed, 29 insertions(+), 20 deletions(-) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 759ccbec9e..d4c886e82b 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1464,6 +1464,35 @@ (define-public python-reproject changing the pixel resolution, orientation, coordinate system.") (license license:bsd-3))) +(define-public python-sgp4 + (package + (name "python-sgp4") + (version "2.21") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sgp4" version)) + (sha256 + (base32 "1vzcrlrlzmhbycdz16m8v241l8zx49vsy81wcd0yjxs80isvhyb1")))) + (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 for computations of the +position and velocity of an earth-orbiting satellite, given the satellite’s +@acronym{TLE, Two-line element set} orbital elements from a source like +@url{CelesTrak, https://celestrak.org/}. + +It implements the most recent version of @acronym{SGP4, Simplified General +Perturbation models}, and is regularly run against the SGP4 test suite to make +sure that its satellite position predictions agree to within 0.1 mm with the +predictions of the standard distribution of the algorithm. This error is far +less than the 1–3 km/day by which satellites themselves deviate from the ideal +orbits described in TLE files.") + (license license:expat))) + (define-public python-sunpy (package (name "python-sunpy") diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index ef4d93500a..dab044d9f7 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -290,26 +290,6 @@ (define-public python-scikit-allel genetic variation data.") (license license:expat))) -(define-public python-sgp4 - (package - (name "python-sgp4") - (version "2.21") - (source - (origin - (method url-fetch) - (uri (pypi-uri "sgp4" version)) - (sha256 - (base32 "1vzcrlrlzmhbycdz16m8v241l8zx49vsy81wcd0yjxs80isvhyb1")))) - (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") -- cgit v1.2.3 From e24b9b42bc9a78bc63e6824e74fc6850e8a90490 Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Wed, 15 Jun 2022 15:39:52 +0000 Subject: gnu: Add python-pydicom. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-science.scm (python-pydicom): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/python-science.scm | 51 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index dab044d9f7..58d127277c 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -20,6 +20,7 @@ ;;; Copyright © 2022 Paul A. Patience ;;; Copyright © 2022 Wiktor Żelazny ;;; Copyright © 2022 Eric Bavier +;;; Copyright © 2022 Antero Mejr ;;; Copyright © 2022 jgart ;;; ;;; This file is part of GNU Guix. @@ -49,6 +50,7 @@ (define-module (gnu packages python-science) #: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) @@ -1488,6 +1490,55 @@ (define-public python-gpy 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") -- cgit v1.2.3