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:
Maxim Cournoyer 2023-04-14 16:57:37 -04:00
commit 3bacd3c76a
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231 changed files with 20528 additions and 7891 deletions

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@ -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