gnu: python-biom-format: Update to 2.1.12.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.12. [arguments]: Remove "relax" phase; update "disable-broken-tests" phase. [propagated-inputs]: Add python-scikit-bio.
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@ -1033,7 +1033,7 @@ (define-public python-bioframe
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(define-public python-biom-format
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(package
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(name "python-biom-format")
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(version "2.1.10")
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(version "2.1.12")
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(source
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(origin
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(method git-fetch)
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@ -1045,25 +1045,22 @@ (define-public python-biom-format
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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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"0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8"))
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"06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
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(modules '((guix build utils)))
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;; Delete generated C files.
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(snippet
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'(for-each delete-file (find-files "." "\\.c")))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(list
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#:phases
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'(modify-phases %standard-phases
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(add-after 'unpack 'use-cython
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(lambda _ (setenv "USE_CYTHON" "1")))
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(add-after 'unpack 'relax
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(lambda _
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(substitute* "setup.py"
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(("pytest < 5.3.4") "pytest"))))
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(add-after 'unpack 'disable-broken-tests
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(lambda _
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(substitute* "biom/tests/test_cli/test_validate_table.py"
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(("^(.+)def test_invalid_hdf5" m indent)
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(substitute* "biom/tests/test_util.py"
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(("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
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(string-append indent
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"@npt.dec.skipif(True, msg='Guix')\n"
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m)))
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@ -1074,13 +1071,14 @@ (define-public python-biom-format
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m))))))))
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(propagated-inputs
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(list python-anndata
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python-numpy
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python-scipy
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python-click
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python-flake8
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python-future
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python-click
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python-h5py
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python-pandas))
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python-numpy
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python-pandas
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python-scikit-bio
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python-scipy))
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(native-inputs
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(list python-cython python-pytest python-pytest-cov python-nose))
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(home-page "http://www.biom-format.org")
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