From da7f89c73780185ae497aabc77a76cb0d81adc33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 May 2021 16:18:13 +0200 Subject: gnu: python-pybedtools: Update to 0.8.2. * gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.2. [arguments]: Remove outdated substitutions; simplify check phase. --- gnu/packages/bioinformatics.scm | 30 ++++++------------------------ 1 file changed, 6 insertions(+), 24 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index de76e67f57..df317df411 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -849,13 +849,13 @@ intended to behave exactly the same as the original BWK awk.") (define-public python-pybedtools (package (name "python-pybedtools") - (version "0.8.1") + (version "0.8.2") (source (origin (method url-fetch) (uri (pypi-uri "pybedtools" version)) (sha256 (base32 - "14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0")))) + "0wc7z8g8prgdx7n5chjva2fdq03wiwhqisjjxzkjg1j5k5ha7151")))) (build-system python-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -868,13 +868,6 @@ intended to behave exactly the same as the original BWK awk.") (modify-phases %standard-phases (add-after 'unpack 'disable-broken-tests (lambda _ - (substitute* "pybedtools/test/test_scripts.py" - ;; This test freezes. - (("def test_intron_exon_reads") - "def _do_not_test_intron_exon_reads") - ;; This test fails in the Python 2 build. - (("def test_venn_mpl") - "def _do_not_test_venn_mpl")) (substitute* "pybedtools/test/test_helpers.py" ;; Requires internet access. (("def test_chromsizes") @@ -886,8 +879,7 @@ 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)) + "def _test_issue_303")))) ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM. ;; build system. ;; Force the Cythonization of C++ files to guard against compilation @@ -908,23 +900,13 @@ intended to behave exactly the same as the original BWK awk.") (invoke "python" "setup.py" "cythonize"))) (replace 'check (lambda _ - (let* ((cwd (getcwd)) - (build-root-directory (string-append cwd "/build/")) + (let* ((build-root-directory (string-append (getcwd) "/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))))) + (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")))) + (string-append build ":" (getenv "PYTHONPATH")))) ;; The tests need to be run from elsewhere... (mkdir-p "/tmp/test") (copy-recursively "pybedtools/test" "/tmp/test") -- cgit v1.2.3