From 155194d97d5ee2499dff063e674e548b8177daea Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 12 Feb 2019 10:32:03 -0500 Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 10 Feb 2019 23:39:25 -0500 Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. * gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.0. [phases]{disable-broken-tests}: Do not disable "test_issue_157" and "test_to_dataframe" tests. Disable the "test_getting_example_beds". {remove-cython-generated-files}: Add phase. {generate-cython-extensions}: Add phase. {check}: Move from python2-pybedtools to here. Add a scripts subdirectory of the build directory to the PATH, so that the tests can call them. Invoke pytest rather than nosetests. [modules]: Move from python2-pybedtools to here. [propagated-inputs]: Depend on the current BEDTOOLS rather than version 1.26. [native-inputs]: Replace python-nose by python-pytest and add python-psutil. --- gnu/packages/bioinformatics.scm | 112 +++++++++++++++++++------------- 1 file changed, 66 insertions(+), 46 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 279d52ae98..d6db02188f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018 Mădălin Ionel Patrașcu +;;; Copyright © 2019 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -612,16 +613,22 @@ intended to behave exactly the same as the original BWK awk.") (define-public python-pybedtools (package (name "python-pybedtools") - (version "0.7.10") + (version "0.8.0") (source (origin (method url-fetch) (uri (pypi-uri "pybedtools" version)) (sha256 (base32 - "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji")))) + "1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf")))) (build-system python-build-system) (arguments - `(#:phases + `(#:modules ((ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26) + (guix build utils) + (guix build python-build-system)) + ;; See https://github.com/daler/pybedtools/issues/192 + #:phases (modify-phases %standard-phases ;; See https://github.com/daler/pybedtools/issues/261 (add-after 'unpack 'disable-broken-tests @@ -631,21 +638,59 @@ intended to behave exactly the same as the original BWK awk.") (substitute* "pybedtools/test/test_scripts.py" (("def test_venn_mpl") "def _do_not_test_venn_mpl")) - ;; Requires internet access. (substitute* "pybedtools/test/test_helpers.py" + ;; Requires internet access. (("def test_chromsizes") - "def _do_not_test_chromsizes")) - ;; FIXME: these two fail for no good reason. - (substitute* "pybedtools/test/test1.py" - (("def test_issue_157") - "def _do_not_test_issue_157") - (("def test_to_dataframe") - "def _do_not_test_to_dataframe")) - #t))))) + "def _do_not_test_chromsizes") + ;; Broken as a result of the workaround used in the check phase + ;; (see: https://github.com/daler/pybedtools/issues/192). + (("def test_getting_example_beds") + "def _do_not_test_getting_example_beds")) + #t)) + ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM. + ;; build system. + ;; Force the Cythonization of C++ files to guard against compilation + ;; problems. + (add-after 'unpack 'remove-cython-generated-files + (lambda _ + (let ((cython-sources (map (cut string-drop-right <> 4) + (find-files "." "\\.pyx$"))) + (c/c++-files (find-files "." "\\.(c|cpp|cxx)$"))) + (define (strip-extension filename) + (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))) + (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") + (with-directory-excursion "/tmp/test" + (invoke "pytest"))))))) (propagated-inputs - ;; Tests don't pass with Bedtools 2.27.1. - ;; See https://github.com/daler/pybedtools/issues/260 - `(("bedtools" ,bedtools-2.26) + `(("bedtools" ,bedtools) ("samtools" ,samtools) ("python-matplotlib" ,python-matplotlib) ("python-pysam" ,python-pysam) @@ -654,9 +699,11 @@ intended to behave exactly the same as the original BWK awk.") `(("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) ("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("kentutils" ,kentutils) ; for bedGraphToBigWig - ("python-six" ,python-six))) + ("kentutils" ,kentutils) ; for bedGraphToBigWig + ("python-six" ,python-six) + ;; For the test suite. + ("python-pytest" ,python-pytest) + ("python-psutil" ,python-psutil))) (home-page "https://pythonhosted.org/pybedtools/") (synopsis "Python wrapper for BEDtools programs") (description @@ -667,34 +714,7 @@ Python.") (license license:gpl2+))) (define-public python2-pybedtools - (let ((pkg (package-with-python2 python-pybedtools))) - (package (inherit pkg) - (arguments - `(#:modules ((ice-9 ftw) - (srfi srfi-1) - (srfi srfi-26) - (guix build utils) - (guix build python-build-system)) - ;; See https://github.com/daler/pybedtools/issues/192 - ,@(substitute-keyword-arguments (package-arguments pkg) - ((#:phases phases) - `(modify-phases ,phases - (replace 'check - (lambda _ - (let ((cwd (getcwd))) - (setenv "PYTHONPATH" - (string-append cwd "/build/" - (find (cut string-prefix? "lib" <>) - (scandir (string-append cwd "/build"))) - ":" (getenv "PYTHONPATH")))) - ;; The tests need to be run from elsewhere... - (mkdir-p "/tmp/test") - (copy-recursively "pybedtools/test" "/tmp/test") - (with-directory-excursion "/tmp/test" - (invoke "nosetests" - ;; This test fails for unknown reasons - "--exclude=.*test_getting_example_beds")) - #t)))))))))) + (package-with-python2 python-pybedtools)) (define-public python-biom-format (package