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gnu: taxtastic: Update to 0.9.2.

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* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2.
[arguments]: Delete 'sanity-check and 'python37-compatibility phases;  adjust
'prepare-directory phase.
This commit is contained in:
Ricardo Wurmus 2021-12-07 15:13:06 +01:00
parent 00ba04020e
commit 16474f85cf
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GPG key ID: 197A5888235FACAC
1 changed files with 7 additions and 13 deletions
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gnu/packages/bioinformatics.scm
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@ -7428,7 +7428,7 @@ Cuffdiff or Ballgown programs.")
(define-public taxtastic (define-public taxtastic
(package (package
(name "taxtastic") (name "taxtastic")
(version "0.8.11") (version "0.9.2")
(source (origin (source (origin
;; The Pypi version does not include tests. ;; The Pypi version does not include tests.
(method git-fetch) (method git-fetch)
@ -7438,15 +7438,13 @@ Cuffdiff or Ballgown programs.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1sv8mkg64jn7zdwf1jj71c16686yrwxk0apb1l8sjszy9p166g0p")))) "1k6wg9ych1j3srnhdny1y4470qlhfg730rb3rm3pq7l7gw62vmgb"))))
(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 'prepare-directory (add-after 'unpack 'prepare-directory
(lambda _ (lambda _
;; The git checkout must be writable for tests.
(for-each make-file-writable (find-files "."))
;; This test fails, but the error is not caught by the test ;; This test fails, but the error is not caught by the test
;; framework, so the tests fail... ;; framework, so the tests fail...
(substitute* "tests/test_taxit.py" (substitute* "tests/test_taxit.py"
@ -7455,20 +7453,16 @@ Cuffdiff or Ballgown programs.")
;; This version file is expected to be created with git describe. ;; This version file is expected to be created with git describe.
(mkdir-p "taxtastic/data") (mkdir-p "taxtastic/data")
(with-output-to-file "taxtastic/data/ver" (with-output-to-file "taxtastic/data/ver"
(lambda () (display ,version))) (lambda () (display ,version)))))
#t))
(add-after 'unpack 'python37-compatibility
(lambda _
(substitute* "taxtastic/utils.py"
(("import csv") "import csv, errno")
(("os.errno") "errno"))
#t))
(replace 'check (replace 'check
;; Note, this fails to run with "-v" as it tries to write to a ;; Note, this fails to run with "-v" as it tries to write to a
;; closed output stream. ;; closed output stream.
(lambda* (#:key tests? #:allow-other-keys) (lambda* (#:key tests? #:allow-other-keys)
(when tests? (when tests?
(invoke "python" "-m" "unittest"))))))) (invoke "python" "-m" "unittest"))))
;; This fails because it cannot find psycopg2 even though it is
;; available.
(delete 'sanity-check))))
(propagated-inputs (propagated-inputs
`(("python-sqlalchemy" ,python-sqlalchemy) `(("python-sqlalchemy" ,python-sqlalchemy)
("python-decorator" ,python-decorator) ("python-decorator" ,python-decorator)