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gnu: python-biom-format: Update to 2.1.12.

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* 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.
This commit is contained in:
Ricardo Wurmus 2022-12-02 21:45:40 +01:00
parent b93e21a213
commit fd44d489b5
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GPG key ID: 197A5888235FACAC
1 changed files with 12 additions and 14 deletions
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26
gnu/packages/bioinformatics.scm
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@ -1033,7 +1033,7 @@ (define-public python-bioframe
(define-public python-biom-format
(package
(name "python-biom-format")
(version "2.1.10")
(version "2.1.12")
(source
(origin
(method git-fetch)
@ -1045,25 +1045,22 @@ (define-public python-biom-format
(file-name (git-file-name name version))
(sha256
(base32
"0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8"))
"06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
(modules '((guix build utils)))
;; Delete generated C files.
(snippet
'(for-each delete-file (find-files "." "\\.c")))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(list
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'use-cython
(lambda _ (setenv "USE_CYTHON" "1")))
(add-after 'unpack 'relax
(lambda _
(substitute* "setup.py"
(("pytest < 5.3.4") "pytest"))))
(add-after 'unpack 'disable-broken-tests
(lambda _
(substitute* "biom/tests/test_cli/test_validate_table.py"
(("^(.+)def test_invalid_hdf5" m indent)
(substitute* "biom/tests/test_util.py"
(("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
(string-append indent
"@npt.dec.skipif(True, msg='Guix')\n"
m)))
@ -1074,13 +1071,14 @@ (define-public python-biom-format
m))))))))
(propagated-inputs
(list python-anndata
python-numpy
python-scipy
python-click
python-flake8
python-future
python-click
python-h5py
python-pandas))
python-numpy
python-pandas
python-scikit-bio
python-scipy))
(native-inputs
(list python-cython python-pytest python-pytest-cov python-nose))
(home-page "http://www.biom-format.org")