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gnu: python-biom-format: Update to 2.1.10.

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* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.
This commit is contained in:
Ricardo Wurmus 2021-12-02 17:56:10 +01:00
parent fab80c3672
commit 32d5fb01f8
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GPG key ID: 197A5888235FACAC
1 changed files with 16 additions and 15 deletions
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gnu/packages/bioinformatics.scm
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@ -1024,7 +1024,7 @@ (define-public python2-pybedtools
(define-public python-biom-format (define-public python-biom-format
(package (package
(name "python-biom-format") (name "python-biom-format")
(version "2.1.7") (version "2.1.10")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -1036,18 +1036,21 @@ (define-public python-biom-format
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v")) "0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet '(begin ;; Delete generated C files.
;; Delete generated C files. (snippet
(for-each delete-file (find-files "." "\\.c")) '(for-each delete-file (find-files "." "\\.c")))))
#t))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:phases `(#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after 'unpack 'use-cython (add-after 'unpack 'use-cython
(lambda _ (setenv "USE_CYTHON" "1") #t)) (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_cli/test_validate_table.py"
@ -1059,24 +1062,22 @@ (define-public python-biom-format
(("^(.+)def test_from_hdf5_issue_731" m indent) (("^(.+)def test_from_hdf5_issue_731" m indent)
(string-append indent (string-append indent
"@npt.dec.skipif(True, msg='Guix')\n" "@npt.dec.skipif(True, msg='Guix')\n"
m))) m)))))
#t))
(add-before 'reset-gzip-timestamps 'make-files-writable (add-before 'reset-gzip-timestamps 'make-files-writable
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))) (let ((out (assoc-ref outputs "out")))
(for-each (lambda (file) (chmod file #o644)) (for-each (lambda (file) (chmod file #o644))
(find-files out "\\.gz")) (find-files out "\\.gz"))))))))
#t))))))
(propagated-inputs (propagated-inputs
`(("python-numpy" ,python-numpy) `(("python-anndata" ,python-anndata)
("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy) ("python-scipy" ,python-scipy)
("python-flake8" ,python-flake8) ("python-flake8" ,python-flake8)
("python-future" ,python-future) ("python-future" ,python-future)
("python-click" ,python-click) ("python-click" ,python-click)
("python-h5py" ,python-h5py) ("python-h5py" ,python-h5py)
;; FIXME: Upgrade to pandas 1.0 when ("python-pandas" ,python-pandas)))
;; https://github.com/biocore/biom-format/issues/837 is resolved.
("python-pandas" ,python-pandas-0.25)))
(native-inputs (native-inputs
`(("python-cython" ,python-cython) `(("python-cython" ,python-cython)
("python-pytest" ,python-pytest) ("python-pytest" ,python-pytest)