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gnu: khmer: Fix build with Python 3.8.

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* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
This commit is contained in:
Ricardo Wurmus 2021-12-02 18:24:31 +01:00
parent 32d5fb01f8
commit 31d372cd8a
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GPG key ID: 197A5888235FACAC
1 changed files with 9 additions and 6 deletions
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gnu/packages/bioinformatics.scm
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@ -5040,23 +5040,26 @@ (define-public khmer
(("# libraries = z,bz2") (("# libraries = z,bz2")
"libraries = z,bz2") "libraries = z,bz2")
(("include:third-party/zlib:third-party/bzip2") (("include:third-party/zlib:third-party/bzip2")
"include:")) "include:"))))))
#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 'set-cc (add-after 'unpack 'set-cc
(lambda _ (setenv "CC" "gcc") #t)) (lambda _ (setenv "CC" "gcc")))
(add-after 'unpack 'python-3.8-compatibility
(lambda _
;; Python 3.8 removed time.clock().
(substitute* "sandbox/sweep-reads.py"
(("time\\.clock")
"time.process_time"))))
(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)
;; Make sure .gz files are writable so that the ;; Make sure .gz files are writable so that the
;; 'reset-gzip-timestamps' phase can do its work. ;; 'reset-gzip-timestamps' phase can do its work.
(let ((out (assoc-ref outputs "out"))) (let ((out (assoc-ref outputs "out")))
(for-each make-file-writable (for-each make-file-writable
(find-files out "\\.gz$")) (find-files out "\\.gz$"))))))))
#t))))))
(native-inputs (native-inputs
`(("python-cython" ,python-cython) `(("python-cython" ,python-cython)
("python-pytest" ,python-pytest) ("python-pytest" ,python-pytest)