gnu: python-pybedtools: Update to 0.8.0 and fix build.
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.
master
Maxim Cournoyer
Ricardo Wurmus
parent
b856a78c94
commit
155194d97d
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@ -12,6 +12,7 @@
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;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
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;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
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;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
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;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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@ -612,16 +613,22 @@ intended to behave exactly the same as the original BWK awk.")
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(define-public python-pybedtools
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(package
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(name "python-pybedtools")
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(version "0.7.10")
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(version "0.8.0")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "pybedtools" version))
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(sha256
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(base32
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"0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji"))))
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"1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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`(#:modules ((ice-9 ftw)
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(srfi srfi-1)
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(srfi srfi-26)
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(guix build utils)
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(guix build python-build-system))
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;; See https://github.com/daler/pybedtools/issues/192
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#:phases
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(modify-phases %standard-phases
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;; See https://github.com/daler/pybedtools/issues/261
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(add-after 'unpack 'disable-broken-tests
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@ -631,21 +638,59 @@ intended to behave exactly the same as the original BWK awk.")
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(substitute* "pybedtools/test/test_scripts.py"
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(("def test_venn_mpl")
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"def _do_not_test_venn_mpl"))
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;; Requires internet access.
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(substitute* "pybedtools/test/test_helpers.py"
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;; Requires internet access.
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(("def test_chromsizes")
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"def _do_not_test_chromsizes"))
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;; FIXME: these two fail for no good reason.
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(substitute* "pybedtools/test/test1.py"
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(("def test_issue_157")
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"def _do_not_test_issue_157")
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(("def test_to_dataframe")
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"def _do_not_test_to_dataframe"))
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#t)))))
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"def _do_not_test_chromsizes")
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;; Broken as a result of the workaround used in the check phase
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;; (see: https://github.com/daler/pybedtools/issues/192).
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(("def test_getting_example_beds")
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"def _do_not_test_getting_example_beds"))
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#t))
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;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
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;; build system.
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;; Force the Cythonization of C++ files to guard against compilation
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;; problems.
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(add-after 'unpack 'remove-cython-generated-files
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(lambda _
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(let ((cython-sources (map (cut string-drop-right <> 4)
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(find-files "." "\\.pyx$")))
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(c/c++-files (find-files "." "\\.(c|cpp|cxx)$")))
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(define (strip-extension filename)
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(string-take filename (string-index-right filename #\.)))
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(define (cythonized? c/c++-file)
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(member (strip-extension c/c++-file) cython-sources))
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(for-each delete-file (filter cythonized? c/c++-files))
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#t)))
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(add-after 'remove-cython-generated-files 'generate-cython-extensions
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(lambda _
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(invoke "python" "setup.py" "cythonize")))
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(replace 'check
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(lambda _
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(let* ((cwd (getcwd))
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(build-root-directory (string-append cwd "/build/"))
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(build (string-append
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build-root-directory
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(find (cut string-prefix? "lib" <>)
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(scandir (string-append
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build-root-directory)))))
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(scripts (string-append
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build-root-directory
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(find (cut string-prefix? "scripts" <>)
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(scandir build-root-directory)))))
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(setenv "PYTHONPATH"
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(string-append build ":" (getenv "PYTHONPATH")))
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;; Executable scripts such as 'intron_exon_reads.py' must be
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;; available in the PATH.
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(setenv "PATH"
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(string-append scripts ":" (getenv "PATH"))))
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;; The tests need to be run from elsewhere...
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(mkdir-p "/tmp/test")
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(copy-recursively "pybedtools/test" "/tmp/test")
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(with-directory-excursion "/tmp/test"
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(invoke "pytest")))))))
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(propagated-inputs
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;; Tests don't pass with Bedtools 2.27.1.
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;; See https://github.com/daler/pybedtools/issues/260
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`(("bedtools" ,bedtools-2.26)
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`(("bedtools" ,bedtools)
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("samtools" ,samtools)
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("python-matplotlib" ,python-matplotlib)
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("python-pysam" ,python-pysam)
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@ -654,9 +699,11 @@ intended to behave exactly the same as the original BWK awk.")
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`(("python-numpy" ,python-numpy)
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("python-pandas" ,python-pandas)
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("python-cython" ,python-cython)
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("python-nose" ,python-nose)
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("kentutils" ,kentutils) ; for bedGraphToBigWig
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("python-six" ,python-six)))
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("kentutils" ,kentutils) ; for bedGraphToBigWig
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("python-six" ,python-six)
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;; For the test suite.
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("python-pytest" ,python-pytest)
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("python-psutil" ,python-psutil)))
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(home-page "https://pythonhosted.org/pybedtools/")
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(synopsis "Python wrapper for BEDtools programs")
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(description
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@ -667,34 +714,7 @@ Python.")
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(license license:gpl2+)))
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(define-public python2-pybedtools
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(let ((pkg (package-with-python2 python-pybedtools)))
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(package (inherit pkg)
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(arguments
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`(#:modules ((ice-9 ftw)
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(srfi srfi-1)
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(srfi srfi-26)
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(guix build utils)
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(guix build python-build-system))
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;; See https://github.com/daler/pybedtools/issues/192
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,@(substitute-keyword-arguments (package-arguments pkg)
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((#:phases phases)
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`(modify-phases ,phases
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(replace 'check
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(lambda _
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(let ((cwd (getcwd)))
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(setenv "PYTHONPATH"
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(string-append cwd "/build/"
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(find (cut string-prefix? "lib" <>)
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(scandir (string-append cwd "/build")))
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":" (getenv "PYTHONPATH"))))
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;; The tests need to be run from elsewhere...
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(mkdir-p "/tmp/test")
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(copy-recursively "pybedtools/test" "/tmp/test")
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(with-directory-excursion "/tmp/test"
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(invoke "nosetests"
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;; This test fails for unknown reasons
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"--exclude=.*test_getting_example_beds"))
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#t))))))))))
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(package-with-python2 python-pybedtools))
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(define-public python-biom-format
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(package
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