gnu: imp: Migrate to Python 3.
* gnu/packages/bioinformatics.scm (imp) [arguments]: Enable tests by removing the #:tests? argument. Specify the arguments to pass to the ctest test running via the #:configure-flags argument. [inputs]: Add cgal and opencv. Remove python-2. Move swig to... [native-inputs]: ...here. Add python-wrapper. [propagated-inputs]: Replace python2-numpy, python2-scipy, python2-pandas, python2-scikit-learn and python2-networkx by python-numpy, python-scipy, python-pandas, python-scikit-learn and python-networkx, respectively.
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@ -12,7 +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, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
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;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
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;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
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;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
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@ -66,6 +66,7 @@ (define-module (gnu packages bioinformatics)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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#:use-module (gnu packages code)
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#:use-module (gnu packages cmake)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages cpio)
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#:use-module (gnu packages cran)
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@ -82,6 +83,7 @@ (define-module (gnu packages bioinformatics)
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#:use-module (gnu packages golang)
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#:use-module (gnu packages glib)
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#:use-module (gnu packages graph)
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#:use-module (gnu packages graphics)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages groff)
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#:use-module (gnu packages gtk)
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@ -91,6 +93,7 @@ (define-module (gnu packages bioinformatics)
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#:use-module (gnu packages haskell-web)
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#:use-module (gnu packages haskell-xyz)
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#:use-module (gnu packages image)
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#:use-module (gnu packages image-processing)
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#:use-module (gnu packages imagemagick)
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#:use-module (gnu packages java)
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#:use-module (gnu packages java-compression)
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@ -11169,23 +11172,44 @@ (define-public imp
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"1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj"))))
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(build-system cmake-build-system)
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(arguments
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`(;; FIXME: Some tests fail because they produce warnings, others fail
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;; because the PYTHONPATH does not include the modeller's directory.
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#:tests? #f))
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`( ;; CMake 3.17 or newer is required for the CMAKE_TEST_ARGUMENTS used
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;; below to have an effect.
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#:cmake ,cmake
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#:configure-flags
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(let ((disabled-tests
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'("expensive" ;exclude expensive tests
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"IMP.modeller" ;fail to import its own modules
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"IMP.parallel-test_sge.py" ;fail in build container
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;; The following test fails non-reproducibly on
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;; an inexact numbers assertion.
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"IMP.em-medium_test_local_fitting.py")))
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(list
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(string-append
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"-DCMAKE_CTEST_ARGUMENTS="
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(string-join
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(list "-L" "-tests?-" ;select only tests
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"-E" (format #f "'(~a)'" (string-join disabled-tests "|")))
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";"))))))
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(native-inputs
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`(("python" ,python-wrapper)
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("swig" ,swig)))
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(inputs
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`(("boost" ,boost)
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("cgal" ,cgal)
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("gsl" ,gsl)
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("swig" ,swig)
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("hdf5" ,hdf5)
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("fftw" ,fftw)
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("eigen" ,eigen)
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("python" ,python-2)))
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;; Enabling MPI causes the build to use all the available memory and
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;; fail (tested on a machine with 32 GiB of RAM).
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;;("mpi" ,openmpi)
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("opencv" ,opencv)))
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(propagated-inputs
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`(("python2-numpy" ,python2-numpy)
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("python2-scipy" ,python2-scipy)
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("python2-pandas" ,python2-pandas)
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("python2-scikit-learn" ,python2-scikit-learn)
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("python2-networkx" ,python2-networkx)))
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`(("python-numpy" ,python-numpy)
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("python-scipy" ,python-scipy)
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("python-pandas" ,python-pandas)
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("python-scikit-learn" ,python-scikit-learn)
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("python-networkx" ,python-networkx)))
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(home-page "https://integrativemodeling.org")
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(synopsis "Integrative modeling platform")
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(description "IMP's broad goal is to contribute to a comprehensive
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