From e7e73f750fa276c66995f3b9967dd2639be19cf8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 23 Nov 2020 11:42:37 -0500 Subject: 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. --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++---------- 1 file changed, 35 insertions(+), 11 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 939dc79d15..bd5a32a9b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu -;;; Copyright © 2019 Maxim Cournoyer +;;; Copyright © 2019, 2020 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling @@ -66,6 +66,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages code) + #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages cran) @@ -82,6 +83,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphics) #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) @@ -91,6 +93,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages haskell-web) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) + #:use-module (gnu packages image-processing) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages java-compression) @@ -11169,23 +11172,44 @@ (define-public imp "1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj")))) (build-system cmake-build-system) (arguments - `(;; FIXME: Some tests fail because they produce warnings, others fail - ;; because the PYTHONPATH does not include the modeller's directory. - #:tests? #f)) + `( ;; CMake 3.17 or newer is required for the CMAKE_TEST_ARGUMENTS used + ;; below to have an effect. + #: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 `(("boost" ,boost) + ("cgal" ,cgal) ("gsl" ,gsl) - ("swig" ,swig) ("hdf5" ,hdf5) ("fftw" ,fftw) ("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 - `(("python2-numpy" ,python2-numpy) - ("python2-scipy" ,python2-scipy) - ("python2-pandas" ,python2-pandas) - ("python2-scikit-learn" ,python2-scikit-learn) - ("python2-networkx" ,python2-networkx))) + `(("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-pandas" ,python-pandas) + ("python-scikit-learn" ,python-scikit-learn) + ("python-networkx" ,python-networkx))) (home-page "https://integrativemodeling.org") (synopsis "Integrative modeling platform") (description "IMP's broad goal is to contribute to a comprehensive -- cgit v1.2.3