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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-12-08 12:00:48 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-12-08 14:31:53 +0100 |
| commit | 298a8d0b89bb44ccb6b7058ded17a55ae831c96a (patch) | |
| tree | 991f021817accee06ce438405c88f3175ae6a493 /gnu/packages/bioinformatics.scm | |
| parent | 9a19e8f6090ab887dbdc09cdebcc00f83b4593f2 (diff) | |
| download | guix-patches-298a8d0b89bb44ccb6b7058ded17a55ae831c96a.tar guix-patches-298a8d0b89bb44ccb6b7058ded17a55ae831c96a.tar.gz | |
gnu: khmer: Cythonize source files.
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove generated files.
[arguments]: Add phase 'do-use-cython to patch the setup.py to generate cpp
files from Cython sources; add 'build-extensions phase; replace 'check phase.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 29 |
1 files changed, 21 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 741e632eb1..d8fb3024ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5082,7 +5082,9 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (("# libraries = z,bz2") "libraries = z,bz2") (("include:third-party/zlib:third-party/bzip2") - "include:")))))) + "include:")) + ;; Delete generated Cython CPP files. + (for-each delete-file (find-files "khmer/_oxli/" "\\.cpp$")))))) (build-system python-build-system) (arguments `(#:phases @@ -5095,13 +5097,24 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (substitute* "sandbox/sweep-reads.py" (("time\\.clock") "time.process_time")))) - (add-before 'reset-gzip-timestamps 'make-files-writable - (lambda* (#:key outputs #:allow-other-keys) - ;; Make sure .gz files are writable so that the - ;; 'reset-gzip-timestamps' phase can do its work. - (let ((out (assoc-ref outputs "out"))) - (for-each make-file-writable - (find-files out "\\.gz$")))))))) + (add-after 'unpack 'do-use-cython + (lambda _ + (substitute* "setup.py" + (("from setuptools import Extension as CyExtension") + "from Cython.Distutils import Extension as CyExtension") + (("from setuptools.command.build_ext import build_ext as _build_ext") + "from Cython.Distutils import build_ext as _build_ext") + (("HAS_CYTHON = False") "HAS_CYTHON = True") + (("cy_ext = 'cpp'") "cy_ext = 'pyx'")))) + (add-before 'build 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace"))) + (replace 'check + (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-v"))))))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) |