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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.
master
Maxim Cournoyer 2020-11-23 11:42:37 -05:00
parent 5458648302
commit e7e73f750f
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1 changed files with 35 additions and 11 deletions
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@ -12,7 +12,7 @@
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
@ -66,6 +66,7 @@
#:use-module (gnu packages boost) #:use-module (gnu packages boost)
#:use-module (gnu packages check) #:use-module (gnu packages check)
#:use-module (gnu packages code) #:use-module (gnu packages code)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression) #:use-module (gnu packages compression)
#:use-module (gnu packages cpio) #:use-module (gnu packages cpio)
#:use-module (gnu packages cran) #:use-module (gnu packages cran)
@ -82,6 +83,7 @@
#:use-module (gnu packages golang) #:use-module (gnu packages golang)
#:use-module (gnu packages glib) #:use-module (gnu packages glib)
#:use-module (gnu packages graph) #:use-module (gnu packages graph)
#:use-module (gnu packages graphics)
#:use-module (gnu packages graphviz) #:use-module (gnu packages graphviz)
#:use-module (gnu packages groff) #:use-module (gnu packages groff)
#:use-module (gnu packages gtk) #:use-module (gnu packages gtk)
@ -91,6 +93,7 @@
#:use-module (gnu packages haskell-web) #:use-module (gnu packages haskell-web)
#:use-module (gnu packages haskell-xyz) #:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages image) #:use-module (gnu packages image)
#:use-module (gnu packages image-processing)
#:use-module (gnu packages imagemagick) #:use-module (gnu packages imagemagick)
#:use-module (gnu packages java) #:use-module (gnu packages java)
#:use-module (gnu packages java-compression) #:use-module (gnu packages java-compression)
@ -11169,23 +11172,44 @@ programs for inferring phylogenies (evolutionary trees).")
"1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj")))) "1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj"))))
(build-system cmake-build-system) (build-system cmake-build-system)
(arguments (arguments
`(;; FIXME: Some tests fail because they produce warnings, others fail `( ;; CMake 3.17 or newer is required for the CMAKE_TEST_ARGUMENTS used
;; because the PYTHONPATH does not include the modeller's directory. ;; below to have an effect.
#:tests? #f)) #:cmake ,cmake
#:configure-flags
(let ((disabled-tests
'("expensive" ;exclude expensive tests
"IMP.modeller" ;fail to import its own modules
"IMP.parallel-test_sge.py" ;fail in build container
;; The following test fails non-reproducibly on
;; an inexact numbers assertion.
"IMP.em-medium_test_local_fitting.py")))
(list
(string-append
"-DCMAKE_CTEST_ARGUMENTS="
(string-join
(list "-L" "-tests?-" ;select only tests
"-E" (format #f "'(~a)'" (string-join disabled-tests "|")))
";"))))))
(native-inputs
`(("python" ,python-wrapper)
("swig" ,swig)))
(inputs (inputs
`(("boost" ,boost) `(("boost" ,boost)
("cgal" ,cgal)
("gsl" ,gsl) ("gsl" ,gsl)
("swig" ,swig)
("hdf5" ,hdf5) ("hdf5" ,hdf5)
("fftw" ,fftw) ("fftw" ,fftw)
("eigen" ,eigen) ("eigen" ,eigen)
("python" ,python-2))) ;; Enabling MPI causes the build to use all the available memory and
;; fail (tested on a machine with 32 GiB of RAM).
;;("mpi" ,openmpi)
("opencv" ,opencv)))
(propagated-inputs (propagated-inputs
`(("python2-numpy" ,python2-numpy) `(("python-numpy" ,python-numpy)
("python2-scipy" ,python2-scipy) ("python-scipy" ,python-scipy)
("python2-pandas" ,python2-pandas) ("python-pandas" ,python-pandas)
("python2-scikit-learn" ,python2-scikit-learn) ("python-scikit-learn" ,python-scikit-learn)
("python2-networkx" ,python2-networkx))) ("python-networkx" ,python-networkx)))
(home-page "https://integrativemodeling.org") (home-page "https://integrativemodeling.org")
(synopsis "Integrative modeling platform") (synopsis "Integrative modeling platform")
(description "IMP's broad goal is to contribute to a comprehensive (description "IMP's broad goal is to contribute to a comprehensive