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author | Maxim Cournoyer <maxim.cournoyer@gmail.com> | 2021-01-22 15:39:14 -0500 |
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committer | Maxim Cournoyer <maxim.cournoyer@gmail.com> | 2021-02-01 11:53:46 -0500 |
commit | 25798ca0e0f7071d41aa7317f8d7f9bb2f294a23 (patch) | |
tree | 788ba3e012ff5cbd45dba4b3a1101bf06ef81119 /gnu | |
parent | 3016f1f21a2354b9df609b0e76246d1f3b9ce209 (diff) | |
download | guix-patches-25798ca0e0f7071d41aa7317f8d7f9bb2f294a23.tar guix-patches-25798ca0e0f7071d41aa7317f8d7f9bb2f294a23.tar.gz |
gnu: python-pybedtools: Streamline following Python build system changes.
* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t.
[phases]{check}: Do not manually set PYTHONPATH.
[arguments]: Remove the '#:modules' argument.
Diffstat (limited to 'gnu')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 29 |
1 files changed, 3 insertions, 26 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 058949618e..1ac6b00e46 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -816,9 +816,7 @@ intended to behave exactly the same as the original BWK awk.") "14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0")))) (build-system python-build-system) (arguments - `(#:modules ((ice-9 ftw) - (srfi srfi-1) - (srfi srfi-26) + `(#:modules ((srfi srfi-26) (guix build utils) (guix build python-build-system)) ;; See https://github.com/daler/pybedtools/issues/192 @@ -844,10 +842,7 @@ intended to behave exactly the same as the original BWK awk.") ;; This issue still occurs on python2 (substitute* "pybedtools/test/test_issues.py" (("def test_issue_303") - "def _test_issue_303")) - #t)) - ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM. - ;; build system. + "def _test_issue_303")))) ;; Force the Cythonization of C++ files to guard against compilation ;; problems. (add-after 'unpack 'remove-cython-generated-files @@ -859,30 +854,12 @@ intended to behave exactly the same as the original BWK awk.") (string-take filename (string-index-right filename #\.))) (define (cythonized? c/c++-file) (member (strip-extension c/c++-file) cython-sources)) - (for-each delete-file (filter cythonized? c/c++-files)) - #t))) + (for-each delete-file (filter cythonized? c/c++-files))))) (add-after 'remove-cython-generated-files 'generate-cython-extensions (lambda _ (invoke "python" "setup.py" "cythonize"))) (replace 'check (lambda _ - (let* ((cwd (getcwd)) - (build-root-directory (string-append cwd "/build/")) - (build (string-append - build-root-directory - (find (cut string-prefix? "lib" <>) - (scandir (string-append - build-root-directory))))) - (scripts (string-append - build-root-directory - (find (cut string-prefix? "scripts" <>) - (scandir build-root-directory))))) - (setenv "PYTHONPATH" - (string-append build ":" (getenv "PYTHONPATH"))) - ;; Executable scripts such as 'intron_exon_reads.py' must be - ;; available in the PATH. - (setenv "PATH" - (string-append scripts ":" (getenv "PATH")))) ;; The tests need to be run from elsewhere... (mkdir-p "/tmp/test") (copy-recursively "pybedtools/test" "/tmp/test") |