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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.
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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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gnu/packages/bioinformatics.scm
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@ -1033,7 +1033,7 @@ use-case, we encourage users to compose functions to achieve their goals.")
(define-public python-biom-format (define-public python-biom-format
(package (package
(name "python-biom-format") (name "python-biom-format")
(version "2.1.10") (version "2.1.12")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -1045,25 +1045,22 @@ use-case, we encourage users to compose functions to achieve their goals.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8")) "06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
(modules '((guix build utils))) (modules '((guix build utils)))
;; Delete generated C files. ;; Delete generated C files.
(snippet (snippet
'(for-each delete-file (find-files "." "\\.c"))))) '(for-each delete-file (find-files "." "\\.c")))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:phases
'(modify-phases %standard-phases
(add-after 'unpack 'use-cython (add-after 'unpack 'use-cython
(lambda _ (setenv "USE_CYTHON" "1"))) (lambda _ (setenv "USE_CYTHON" "1")))
(add-after 'unpack 'relax
(lambda _
(substitute* "setup.py"
(("pytest < 5.3.4") "pytest"))))
(add-after 'unpack 'disable-broken-tests (add-after 'unpack 'disable-broken-tests
(lambda _ (lambda _
(substitute* "biom/tests/test_cli/test_validate_table.py" (substitute* "biom/tests/test_util.py"
(("^(.+)def test_invalid_hdf5" m indent) (("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
(string-append indent (string-append indent
"@npt.dec.skipif(True, msg='Guix')\n" "@npt.dec.skipif(True, msg='Guix')\n"
m))) m)))
@ -1074,13 +1071,14 @@ use-case, we encourage users to compose functions to achieve their goals.")
m)))))))) m))))))))
(propagated-inputs (propagated-inputs
(list python-anndata (list python-anndata
python-numpy python-click
python-scipy
python-flake8 python-flake8
python-future python-future
python-click
python-h5py python-h5py
python-pandas)) python-numpy
python-pandas
python-scikit-bio
python-scipy))
(native-inputs (native-inputs
(list python-cython python-pytest python-pytest-cov python-nose)) (list python-cython python-pytest python-pytest-cov python-nose))
(home-page "http://www.biom-format.org") (home-page "http://www.biom-format.org")