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authorMaxim Cournoyer <maxim.cournoyer@gmail.com>2020-11-23 11:42:37 -0500
committerMaxim Cournoyer <maxim.cournoyer@gmail.com>2020-11-24 02:20:31 -0500
commite7e73f750fa276c66995f3b9967dd2639be19cf8 (patch)
tree6781532a43c14a2d3546de7627fa886596703e5c
parent5458648302ca3ae4a60cde3ac3f94691d3afa039 (diff)
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.
-rw-r--r--gnu/packages/bioinformatics.scm46
1 files 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 <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; 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 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
@@ -66,6 +66,7 @@
#: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 @@
#: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 @@
#: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 @@ programs for inferring phylogenies (evolutionary trees).")
"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