diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 165 |
1 files changed, 120 insertions, 45 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 37beb5ed61..c0a1c4794f 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> @@ -158,6 +158,57 @@ the SciPy stack. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.") (license license:bsd-3))) +(define-public python-scikit-allel + (package + (name "python-scikit-allel") + (version "1.3.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scikit-allel" version)) + (sha256 + (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + (string-append + ;; AttributeError: 'Dataset' object has no attribute 'asstr' + "not test_vcf_to_hdf5" + " and not test_vcf_to_hdf5_exclude" + " and not test_vcf_to_hdf5_rename" + " and not test_vcf_to_hdf5_group" + " and not test_vcf_to_hdf5_ann" + ;; Does not work with recent hmmlearn + " and not test_roh_mhmm_0pct" + " and not test_roh_mhmm_100pct")) + #:phases + '(modify-phases %standard-phases + (add-before 'check 'build-ext + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs + (list python-dask + python-numpy)) + (native-inputs + (list python-cython + ;; The following are all needed for the tests + htslib + python-h5py + python-hmmlearn + python-numexpr + python-pytest + python-scipy + python-setuptools-scm + python-zarr)) + (home-page "https://github.com/cggh/scikit-allel") + (synopsis "Explore and analyze genetic variation data") + (description + "This package provides utilities for exploratory analysis of large scale +genetic variation data.") + (license license:expat))) + (define-public python-scikit-fuzzy (package (name "python-scikit-fuzzy") @@ -234,53 +285,33 @@ logic, also known as grey logic.") "Scikit-image is a collection of algorithms for image processing.") (license license:bsd-3))) -(define-public python-scikit-allel +(define-public python-scikit-optimize (package - (name "python-scikit-allel") - (version "1.3.5") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scikit-allel" version)) - (sha256 - (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj")))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "python" "setup.py" "build_ext" "--inplace") - (invoke "python" "-m" "pytest" "-v" "allel" - ;; AttributeError: 'Dataset' object has no attribute 'asstr' - "-k" (string-append - "not test_vcf_to_hdf5" - " and not test_vcf_to_hdf5_exclude" - " and not test_vcf_to_hdf5_rename" - " and not test_vcf_to_hdf5_group" - " and not test_vcf_to_hdf5_ann")))))))) + (name "python-scikit-optimize") + (version "0.9.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "scikit-optimize" version)) + (sha256 + (base32 + "0230ya8bwrzxjwcy2vz23a3hg6caggnnmg2vq1f9zz2797kckn3p")))) + (build-system pyproject-build-system) (propagated-inputs - (list python-dask - python-numpy)) + (list python-joblib + python-matplotlib + python-numpy + python-pyaml + python-scikit-learn + python-scipy)) (native-inputs - (list python-cython - ;; The following are all needed for the tests - htslib - python-h5py - python-hmmlearn - python-numexpr - python-pytest - python-scipy - python-setuptools-scm - python-zarr)) - (home-page "https://github.com/cggh/scikit-allel") - (synopsis "Explore and analyze genetic variation data") - (description - "This package provides utilities for exploratory analysis of large scale -genetic variation data.") - (license license:expat))) + (list python-pytest)) + (home-page "https://scikit-optimize.github.io/") + (synopsis "Sequential model-based optimization toolbox") + (description "Scikit-Optimize, or @code{skopt}, is a simple and efficient +library to minimize (very) expensive and noisy black-box functions. It +implements several methods for sequential model-based optimization. +@code{skopt} aims to be accessible and easy to use in many contexts.") + (license license:bsd-3))) (define-public python-trimesh (package @@ -1677,6 +1708,50 @@ Out-of-Core DataFrames (similar to Pandas), to visualize and explore big tabular datasets. This package provides the core modules of Vaex.") (license license:expat))) +(define-public python-pylems + (package + (name "python-pylems") + (version "0.6.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "PyLEMS" version)) + (sha256 + (base32 + "074azbyivjbwi61fs5p8z9n6d8nk8xw6fmln1www13z1dccb3740")))) + (build-system python-build-system) + (propagated-inputs (list python-lxml)) + (home-page "https://github.com/LEMS/pylems") + (synopsis + "Python support for the Low Entropy Model Specification language (LEMS)") + (description + "A LEMS simulator written in Python which can be used to run +NeuroML2 models.") + (license license:lgpl3))) + +(define-public python-libneuroml + (package + (name "python-libneuroml") + (version "0.4.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/NeuralEnsemble/libNeuroML.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0mrm4rd6x1sm6hkvhk20mkqp9q53sl3lbvq6hqzyymkw1iqq6bhy")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-lxml python-six)) + (native-inputs (list python-pytest python-numpy python-tables)) + (home-page "https://libneuroml.readthedocs.org/en/latest/") + (synopsis + "Python library for working with NeuroML descriptions of neuronal models") + (description + "This package provides a Python library for working with NeuroML descriptions of +neuronal models") + (license license:bsd-3))) + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar |