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Merge branch 'master' into core-updates.
Conflicts: gnu/local.mk gnu/packages/build-tools.scm gnu/packages/certs.scm gnu/packages/check.scm gnu/packages/compression.scm gnu/packages/cups.scm gnu/packages/fontutils.scm gnu/packages/gnuzilla.scm gnu/packages/guile.scm gnu/packages/ibus.scm gnu/packages/image-processing.scm gnu/packages/linux.scm gnu/packages/music.scm gnu/packages/nss.scm gnu/packages/pdf.scm gnu/packages/python-xyz.scm gnu/packages/qt.scm gnu/packages/ruby.scm gnu/packages/shells.scm gnu/packages/tex.scm gnu/packages/video.scm gnu/packages/vulkan.scm gnu/packages/web.scm gnu/packages/webkit.scm gnu/packages/wm.scm
This commit is contained in:
commit
3bacd3c76a
231 changed files with 20528 additions and 7891 deletions
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@ -1,5 +1,5 @@
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015, 2016, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
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;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
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@ -158,6 +158,57 @@ the SciPy stack. It provides many user-friendly and efficient numerical
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routines such as routines for numerical integration and optimization.")
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(license license:bsd-3)))
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(define-public python-scikit-allel
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(package
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(name "python-scikit-allel")
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(version "1.3.5")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scikit-allel" version))
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(sha256
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(base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:test-flags
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'(list "-k"
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(string-append
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;; AttributeError: 'Dataset' object has no attribute 'asstr'
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"not test_vcf_to_hdf5"
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" and not test_vcf_to_hdf5_exclude"
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" and not test_vcf_to_hdf5_rename"
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" and not test_vcf_to_hdf5_group"
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" and not test_vcf_to_hdf5_ann"
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;; Does not work with recent hmmlearn
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" and not test_roh_mhmm_0pct"
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" and not test_roh_mhmm_100pct"))
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#:phases
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'(modify-phases %standard-phases
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(add-before 'check 'build-ext
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(lambda _
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(invoke "python" "setup.py" "build_ext" "--inplace"))))))
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(propagated-inputs
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(list python-dask
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python-numpy))
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(native-inputs
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(list python-cython
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;; The following are all needed for the tests
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htslib
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python-h5py
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python-hmmlearn
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python-numexpr
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python-pytest
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python-scipy
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python-setuptools-scm
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python-zarr))
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(home-page "https://github.com/cggh/scikit-allel")
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(synopsis "Explore and analyze genetic variation data")
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(description
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"This package provides utilities for exploratory analysis of large scale
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genetic variation data.")
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(license license:expat)))
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(define-public python-scikit-fuzzy
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(package
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(name "python-scikit-fuzzy")
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@ -234,53 +285,33 @@ logic, also known as grey logic.")
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"Scikit-image is a collection of algorithms for image processing.")
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(license license:bsd-3)))
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(define-public python-scikit-allel
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(define-public python-scikit-optimize
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(package
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(name "python-scikit-allel")
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(version "1.3.5")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scikit-allel" version))
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(sha256
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(base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
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(build-system python-build-system)
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(arguments
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(list
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#:phases
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#~(modify-phases %standard-phases
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(invoke "python" "setup.py" "build_ext" "--inplace")
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(invoke "python" "-m" "pytest" "-v" "allel"
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;; AttributeError: 'Dataset' object has no attribute 'asstr'
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"-k" (string-append
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"not test_vcf_to_hdf5"
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" and not test_vcf_to_hdf5_exclude"
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" and not test_vcf_to_hdf5_rename"
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" and not test_vcf_to_hdf5_group"
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" and not test_vcf_to_hdf5_ann"))))))))
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(name "python-scikit-optimize")
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(version "0.9.0")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "scikit-optimize" version))
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(sha256
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(base32
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"0230ya8bwrzxjwcy2vz23a3hg6caggnnmg2vq1f9zz2797kckn3p"))))
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(build-system pyproject-build-system)
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(propagated-inputs
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(list python-dask
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python-numpy))
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(list python-joblib
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python-matplotlib
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python-numpy
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python-pyaml
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python-scikit-learn
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python-scipy))
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(native-inputs
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(list python-cython
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;; The following are all needed for the tests
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htslib
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python-h5py
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python-hmmlearn
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python-numexpr
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python-pytest
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python-scipy
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python-setuptools-scm
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python-zarr))
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(home-page "https://github.com/cggh/scikit-allel")
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(synopsis "Explore and analyze genetic variation data")
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(description
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"This package provides utilities for exploratory analysis of large scale
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genetic variation data.")
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(license license:expat)))
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(list python-pytest))
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(home-page "https://scikit-optimize.github.io/")
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(synopsis "Sequential model-based optimization toolbox")
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(description "Scikit-Optimize, or @code{skopt}, is a simple and efficient
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library to minimize (very) expensive and noisy black-box functions. It
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implements several methods for sequential model-based optimization.
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@code{skopt} aims to be accessible and easy to use in many contexts.")
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(license license:bsd-3)))
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(define-public python-trimesh
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(package
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@ -1677,6 +1708,50 @@ Out-of-Core DataFrames (similar to Pandas), to visualize and explore big
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tabular datasets. This package provides the core modules of Vaex.")
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(license license:expat)))
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(define-public python-pylems
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(package
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(name "python-pylems")
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(version "0.6.0")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "PyLEMS" version))
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(sha256
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(base32
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"074azbyivjbwi61fs5p8z9n6d8nk8xw6fmln1www13z1dccb3740"))))
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(build-system python-build-system)
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(propagated-inputs (list python-lxml))
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(home-page "https://github.com/LEMS/pylems")
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(synopsis
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"Python support for the Low Entropy Model Specification language (LEMS)")
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(description
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"A LEMS simulator written in Python which can be used to run
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NeuroML2 models.")
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(license license:lgpl3)))
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(define-public python-libneuroml
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(package
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(name "python-libneuroml")
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(version "0.4.1")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/NeuralEnsemble/libNeuroML.git")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0mrm4rd6x1sm6hkvhk20mkqp9q53sl3lbvq6hqzyymkw1iqq6bhy"))))
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(build-system pyproject-build-system)
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(propagated-inputs (list python-lxml python-six))
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(native-inputs (list python-pytest python-numpy python-tables))
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(home-page "https://libneuroml.readthedocs.org/en/latest/")
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(synopsis
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"Python library for working with NeuroML descriptions of neuronal models")
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(description
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"This package provides a Python library for working with NeuroML descriptions of
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neuronal models")
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(license license:bsd-3)))
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;;;
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;;; Avoid adding new packages to the end of this file. To reduce the chances
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;;; of a merge conflict, place them above by existing packages with similar
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