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07/09: gnu: python-pysam: Enable tests.
From: |
Ben Woodcroft |
Subject: |
07/09: gnu: python-pysam: Enable tests. |
Date: |
Tue, 27 Sep 2016 10:50:53 +0000 (UTC) |
benwoodcroft pushed a commit to branch master
in repository guix.
commit f536dce522e08315c468f60448507af2cac619ac
Author: Marius Bakke <address@hidden>
Date: Thu Sep 22 14:11:59 2016 +0100
gnu: python-pysam: Enable tests.
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.
---
gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++------
1 file changed, 30 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3ca6fd6..078b0a6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1351,18 +1351,21 @@ multiple sequence alignments.")
(version "0.9.1.4")
(source (origin
(method url-fetch)
- (uri (pypi-uri "pysam" version))
+ ;; Test data is missing on PyPi.
+ (uri (string-append
+ "https://github.com/pysam-developers/pysam/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1i1djacqbr88y7w18b4aa78zxnsyr4sz7yqdq2spi7gs0y6pzvjn"))
+ "0y41ssbg6nvn2jgcbnrvkzblpjcwszaiv1rgyd8dwzjkrbfsgsmc"))
(modules '((guix build utils)))
(snippet
;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
'(delete-file-recursively "htslib"))))
(build-system python-build-system)
(arguments
- `(#:tests? #f ; tests are excluded in the manifest
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(add-before 'build 'set-flags
(lambda* (#:key inputs #:allow-other-keys)
@@ -1373,7 +1376,24 @@ multiple sequence alignments.")
(string-append (assoc-ref inputs "htslib") "/include"))
(setenv "LDFLAGS" "-lncurses")
(setenv "CFLAGS" "-D_CURSES_LIB=1")
- #t)))))
+ #t))
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PYTHONPATH"
+ (string-append
+ (getenv "PYTHONPATH")
+ ":" (assoc-ref outputs "out")
+ "/lib/python"
+ (string-take (string-take-right
+ (assoc-ref inputs "python") 5) 3)
+ "/site-packages"))
+ ;; Step out of source dir so python does not import from CWD.
+ (chdir "tests")
+ (setenv "HOME" "/tmp")
+ (and (zero? (system* "make" "-C" "pysam_data"))
+ (zero? (system* "make" "-C" "cbcf_data"))
+ (zero? (system* "nosetests" "-v"))))))))
(propagated-inputs
`(("htslib" ,htslib))) ; Included from installed header files.
(inputs
@@ -1381,7 +1401,11 @@ multiple sequence alignments.")
("zlib" ,zlib)))
(native-inputs
`(("python-cython" ,python-cython)
- ("python-setuptools" ,python-setuptools)))
+ ("python-setuptools" ,python-setuptools)
+ ;; Dependencies below are are for tests only.
+ ("samtools" ,samtools)
+ ("bcftools" ,bcftools)
+ ("python-nose" ,python-nose)))
(home-page "https://github.com/pysam-developers/pysam")
(synopsis "Python bindings to the SAMtools C API")
(description
- branch master updated (8a54c0e -> 99caa6f), Ben Woodcroft, 2016/09/27
- 01/09: gnu: python-pysam: Update to 0.9.1.4., Ben Woodcroft, 2016/09/27
- 06/09: gnu: python-pysam: Delete bundled htslib., Ben Woodcroft, 2016/09/27
- 03/09: gnu: python2-pbcore: Update to 1.2.10., Ben Woodcroft, 2016/09/27
- 09/09: gnu: python-plastid: Update to 1.4.6., Ben Woodcroft, 2016/09/27
- 08/09: gnu: Add python-termcolor., Ben Woodcroft, 2016/09/27
- 07/09: gnu: python-pysam: Enable tests.,
Ben Woodcroft <=
- 05/09: gnu: python-pysam: Use 'modify-phases'., Ben Woodcroft, 2016/09/27
- 02/09: gnu: Add python-pyxb., Ben Woodcroft, 2016/09/27
- 04/09: gnu: Add bcftools., Ben Woodcroft, 2016/09/27