From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
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 | 114 +++++++++++++++++++-------------
1 file changed, 67 insertions(+), 47 deletions(-)
@@ -12,6 +12,7 @@
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; 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)))))
- (propagated-inputs
- ;; Tests don't pass with Bedtools 2.27.1.
- ;; See https://github.com/daler/pybedtools/issues/260
- `(("bedtools" ,bedtools-2.26)
+ "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
+ `(("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
--
2.20.1