01/01: gnu: multiqc: Update to 0.9.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a29929b32caf9e437d18bdb0cd4d1b22bc096fed
Author: Ben Woodcroft <address@hidden>
Date:   Fri Dec 30 17:21:37 2016 +1000

    gnu: multiqc: Update to 0.9.
    
    Suggested by Raoul Bonnal <address@hidden>.
    
    * gnu/packages/bioinformatics.scm (multiqc): Update to 0.9.
    [origin]: Add patch.
    * gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file.
    * gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                           |    1 +
 gnu/packages/bioinformatics.scm                        |    9 +++++++--
 .../patches/multiqc-fix-git-subprocess-error.patch     |   16 ++++++++++++++++
 3 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 38c1b0b..b7c182f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -730,6 +730,7 @@ dist_patch_DATA =                                           
\
   %D%/packages/patches/mpc123-initialize-ao.patch              \
   %D%/packages/patches/mplayer2-theora-fix.patch               \
   %D%/packages/patches/module-init-tools-moduledir.patch       \
+  %D%/packages/patches/multiqc-fix-git-subprocess-error.patch  \
   %D%/packages/patches/mumps-build-parallelism.patch           \
   %D%/packages/patches/mupdf-build-with-openjpeg-2.1.patch     \
   %D%/packages/patches/mupen64plus-ui-console-notice.patch     \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 07c4a0a..54c8ce0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7855,15 +7855,20 @@ replacement for strverscmp.")
 (define-public multiqc
   (package
     (name "multiqc")
-    (version "0.6")
+    (version "0.9")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "multiqc" version))
        (sha256
         (base32
-         "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy"))))
+         "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny"))
+       (patches (search-patches "multiqc-fix-git-subprocess-error.patch"))))
     (build-system python-build-system)
+    (arguments
+     ;; Tests are to be introduced in the next version, see
+     ;; https://github.com/ewels/MultiQC/issues/376
+     `(#:tests? #f))
     (propagated-inputs
      `(("python-jinja2" ,python-jinja2)
        ("python-simplejson" ,python-simplejson)
diff --git a/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch 
b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
new file mode 100644
index 0000000..87be614
--- /dev/null
+++ b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
@@ -0,0 +1,16 @@
+Without this patch, the incorrect exception is caught when 'git' is not in
+PATH.  See https://github.com/ewels/MultiQC/pull/377.
+
+diff --git a/multiqc/utils/config.py b/multiqc/utils/config.py
+index 01fa554..4a11793 100755
+--- a/multiqc/utils/config.py
++++ b/multiqc/utils/config.py
+@@ -28,7 +28,7 @@ try:
+     git_hash = subprocess.check_output(['git', 'rev-parse', 'HEAD'], 
stderr=subprocess.STDOUT)
+     git_hash_short = git_hash[:7]
+     version = '{} ({})'.format(version, git_hash_short)
+-except subprocess.CalledProcessError:
++except (subprocess.CalledProcessError, FileNotFoundError):
+     pass
+ os.chdir(cwd)
+