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gnu: python-scikit-allel: Use pyproject-build-system.

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* gnu/packages/python-science.scm (python-scikit-allel): Move up to create
alphabetic order.
[build-system]: Use pyproject-build-system.
[arguments]: Provide test flags instead of overriding 'check phase; split out
build step into new 'build-ext phase.  Disable roh_mhmm tests.
This commit is contained in:
Ricardo Wurmus 2023-03-24 18:23:01 +01:00
parent 6d132c5ebf
commit 896982f357
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1 changed files with 52 additions and 49 deletions
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101
gnu/packages/python-science.scm
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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>
@ -169,6 +169,57 @@ 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")
@ -273,54 +324,6 @@ 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-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 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"))))))))
(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-trimesh
(package
(name "python-trimesh")