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gnu: python-bed-reader: Improve phases' style.

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* gnu/packages/bioinformatics.scm (python-bed-reader)
[arguments]{phases}: Improve phases 'install-python-library and
'check-python with site-packages procedure.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
This commit is contained in:
Nicolas Graves 2025-04-22 16:00:31 +02:00 • committed by Sharlatan Hellseher
parent 7118f9fecc
commit bfdf6a85b8
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1 changed files with 8 additions and 14 deletions
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gnu/packages/bioinformatics.scm
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@ -2333,26 +2333,20 @@ version = ~s
(add-after 'build-python-module 'install-python-module
(assoc-ref py:%standard-phases 'install))
(add-after 'install-python-module 'install-python-library
(lambda _
(let ((site (string-append #$output "/lib/python"
#$(version-major+minor
(package-version python))
"/site-packages/")))
(mkdir-p (string-append site "bed_reader"))
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((site (py:site-packages inputs outputs)))
(mkdir-p (string-append site "/bed_reader"))
(copy-file "target/release/libbed_reader.so"
(string-append site "bed_reader/bed_reader.so")))))
(string-append site "/bed_reader/bed_reader.so")))))
(add-after 'install-python-library 'add-install-to-pythonpath
(assoc-ref py:%standard-phases 'add-install-to-pythonpath))
(add-after 'add-install-to-pythonpath 'check-python
(lambda* (#:key tests? #:allow-other-keys)
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(let ((site (string-append #$output "/lib/python"
#$(version-major+minor
(package-version python))
"/site-packages/"))
(let ((site (py:site-packages inputs outputs))
(data-dir "bed_reader/tests/data"))
(symlink (canonicalize-path data-dir)
(string-append site data-dir))
(string-append site "/" data-dir))
(invoke "pytest" "-v" #$output
;; These test require a 84 GB file.
"-k" (string-join
@ -2363,7 +2357,7 @@ version = ~s
"test_optional_dependencies")
" and not "))
(delete-file-recursively
(string-append site "bed_reader/tests"))
(string-append site "/bed_reader/tests"))
(delete-file-recursively
(string-append #$output "/.pytest_cache")))))))))
(native-inputs (list python-pytest