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gnu: taxtastic: Update to 0.11.1.

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* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.11.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore failing test.
{phases}: Improve style with gexp. Update phase
'prepare-directory. Improve phase 'check with test-flags inclusion.
[native-inputs]: Add python-setuptools, python-wheel.
[propagated-inputs]: Sort inputs. Replace python-psycopg2 by both
python-psycopg and python-psycopg2-binary. Add python-sqlparse.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
This commit is contained in:
Nicolas Graves 2025-03-31 08:18:41 +02:00 • committed by Andreas Enge
parent 5139f5e47f
commit a5d3be8a89
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1 changed files with 37 additions and 32 deletions
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@ -12432,7 +12432,7 @@ Cuffdiff or Ballgown programs.")
(define-public taxtastic
(package
(name "taxtastic")
(version "0.9.2")
(version "0.11.1")
(source (origin
;; The Pypi version does not include tests.
(method git-fetch)
@ -12442,42 +12442,47 @@ Cuffdiff or Ballgown programs.")
(file-name (git-file-name name version))
(sha256
(base32
"1k6wg9ych1j3srnhdny1y4470qlhfg730rb3rm3pq7l7gw62vmgb"))))
(build-system python-build-system)
"18h3vlyx9qp7xymd8ra6jn5h0vzlpzgcd75kslqyv2qcg1a7scc4"))))
(build-system pyproject-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'prepare-directory
(lambda _
;; This test fails, but the error is not caught by the test
;; framework, so the tests fail...
(substitute* "tests/test_taxit.py"
(("self.cmd_fails\\(''\\)")
"self.cmd_fails('nothing')"))
;; This version file is expected to be created with git describe.
(mkdir-p "taxtastic/data")
(with-output-to-file "taxtastic/data/ver"
(lambda () (display ,version)))))
(replace 'check
;; Note, this fails to run with "-v" as it tries to write to a
;; closed output stream.
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "-m" "unittest"))))
;; This fails because it cannot find psycopg2 even though it is
;; available.
(delete 'sanity-check))))
(list
#:test-flags #~(list "-k" "not test_new_nodes02")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'prepare-directory
(lambda _
;; This package is unknown to pypi.
(substitute* '("requirements.txt" "setup.py")
((".*psycopg-binary.*") ""))
;; This test fails, but the error is not caught by the test
;; framework, so the tests fail...
(substitute* "tests/test_taxit.py"
(("self.cmd_fails\\(''\\)")
"self.cmd_fails('nothing')"))
;; This version file is expected to be created with git describe.
(mkdir-p "taxtastic/data")
(with-output-to-file "taxtastic/data/ver"
(lambda () (display #$version)))))
(replace 'check
;; Note, this fails to run with "-v" as it tries to write to a
;; closed output stream.
(lambda* (#:key tests? test-flags #:allow-other-keys)
(when tests?
(apply invoke "python" "-m" "unittest" test-flags)))))))
(native-inputs
(list python-setuptools python-wheel))
(propagated-inputs
(list python-sqlalchemy
(list python-biopython
python-decorator
python-biopython
python-pandas
python-psycopg2
python-dendropy
python-fastalite
python-pyyaml
python-six
python-jinja2
python-dendropy))
python-pandas
python-psycopg
python-psycopg2-binary
python-pyyaml
python-sqlalchemy-2
python-sqlparse))
(home-page "https://github.com/fhcrc/taxtastic")
(synopsis "Tools for taxonomic naming and annotation")
(description