branch master updated (3aeb6e1 -> 6ac0a0f)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  3aeb6e1   gnu: Add ruby-spring.
   new  6ac0a0f   gnu: diamond: Update to 0.8.5.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

02/02: gnu: Add ruby-spring.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 3aeb6e1d1acfeeae61739fbaeeb6e94848557436
Author: Matthew Jordan 
Date:   Tue May 31 07:29:24 2016 -0400

gnu: Add ruby-spring.

* gnu/packages/rails.scm (ruby-spring): New variable.
---
 gnu/packages/rails.scm |   38 ++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/rails.scm b/gnu/packages/rails.scm
index 83abc65..e1e14f5 100644
--- a/gnu/packages/rails.scm
+++ b/gnu/packages/rails.scm
@@ -23,6 +23,44 @@
   #:use-module (gnu packages ruby)
   #:use-module (guix build-system ruby))
 
+(define-public ruby-spring
+  (package
+(name "ruby-spring")
+(version "1.7.1")
+(source
+ (origin
+   (method url-fetch)
+   (uri
+(string-append "https://github.com/rails/spring/archive/v;
+   version ".tar.gz"))
+   (file-name (string-append name "-" version ".tar.gz"))
+   (sha256
+(base32
+ "0czc4mkwfngcqmna49a0l98f6wlhdq2i8gwr63lrmk90d9k25x1n"
+(build-system ruby-build-system)
+(arguments
+ `(#:test-target "test:unit"
+   #:phases
+   (modify-phases %standard-phases
+ (add-before 'check 'remove-bump
+   (lambda _
+ (substitute* "spring.gemspec"
+   (("gem.add_development_dependency 'bump'") ""))
+ (substitute* "Rakefile"
+   (("require \\\"bump/tasks\\\"") ""))
+ #t)
+(native-inputs
+ `(("bundler" ,bundler)
+   ("ruby-activesupport" ,ruby-activesupport)))
+(synopsis "Ruby on Rails application preloader")
+(description
+ "Spring is a Ruby on Rails application preloader.  It speeds up
+development by keeping your application running in the background so the
+application does need to boot it every time you run a test, rake task or
+migration.")
+(home-page "https://github.com/rails/spring;)
+(license license:expat)))
+
 (define-public ruby-debug-inspector
   (package
 (name "ruby-debug-inspector")

branch master updated (1c5ee41 -> 3aeb6e1)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  1c5ee41   gnu: imagemagick: Update to 6.9.4-7.
   new  90322fd   gnu: Add ruby-debug-inspector.
   new  3aeb6e1   gnu: Add ruby-spring.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/local.mk   |1 +
 gnu/packages/rails.scm |   95 
 2 files changed, 96 insertions(+)
 create mode 100644 gnu/packages/rails.scm

01/01: gnu: Update diamond to 0.8.3.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 9fcc3509a7af4348d855141e60501d9728fd6b6f
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat May 28 23:44:16 2016 +1000

gnu: Update diamond to 0.8.3.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3.
---
 gnu/packages/bioinformatics.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dae162e..11e74c6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1482,7 +1482,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.8.1")
+(version "0.8.3")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -1491,7 +1491,7 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"1dqancz32c2l7w1b2vkvh5zqa2jnf99j1c41djnx1l8pxn044zdc"
+"0z9sm46bivz0ghwg8kajizgiigv8dnz4w7cyzsg8wcsm9h2z6zyc"
 (build-system cmake-build-system)
 (arguments
  '(#:tests? #f ; no "check" target

06/10: gnu: ruby-mini-portile-2: Update to 2.1.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 59884b71e38fce4ba862d67d7732dc63c3ad50cd
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat May 21 23:05:18 2016 +1000

gnu: ruby-mini-portile-2: Update to 2.1.0.

* gnu/packages/ruby.scm (ruby-mini-portile-2): Update to 2.1.0.
---
 gnu/packages/ruby.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index de858fb..5c52e32 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1871,13 +1871,13 @@ to reproduce user environments.")
 
 (define-public ruby-mini-portile-2
   (package (inherit ruby-mini-portile)
-(version "2.0.0")
+(version "2.1.0")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "mini_portile2" version))
   (sha256
(base32
-"056drbn5m4khdxly1asmiik14nyllswr6sh3wallvsywwdiryz8l"))
+"1y25adxb1hgg1wb2rn20g3vl07qziq6fz364jc5694611zz863hb"))
 
 (define-public ruby-nokogiri
   (package

04/10: gnu: ruby-shoulda-matchers: Update to 3.1.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 80756fa66b853fb3ab2f8a7886268a64b5aac6e6
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat May 21 23:01:37 2016 +1000

gnu: ruby-shoulda-matchers: Update to 3.1.1.

* gnu/packages/ruby.scm (ruby-shoulda-matchers): Update to 3.1.1.
[arguments]: Remove 'fix-import' phase.
---
 gnu/packages/ruby.scm |   12 ++--
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 1bd3e93..8f43ec6 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3271,26 +3271,18 @@ names.")
 (define-public ruby-shoulda-matchers
   (package
 (name "ruby-shoulda-matchers")
-(version "3.0.1")
+(version "3.1.1")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "shoulda-matchers" version))
(sha256
 (base32
- "1agabvb8i39mjrp3kb78nvhl41xk1i258hdwdlj0fm8nj9yzn1jb"
+ "1cf6d2d9br82vylr9p362yk9cfrd14jz8v77n0yb0lbcxdbk7xzq"
 (build-system ruby-build-system)
 (arguments
  `(#:phases
(modify-phases %standard-phases
- (add-before 'build 'fix-import
-   (lambda _
- ;; A presumed bug reported upstream at
- ;; https://github.com/thoughtbot/shoulda-matchers/pull/871
- (substitute* (string-append  "lib/shoulda/matchers/active_model/"
-  "validate_inclusion_of_matcher.rb")
-   (("^require 'bigdecimal'")
-"require 'bigdecimal'; require 'date'"
  (replace 'check
(lambda _
  ;; Do not run tests to avoid circular dependence with rails.  
Instead

01/10: guix: ruby-build-system: Extract gemspec during 'extract-gemspec'.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 25c288cbf12925e0f079a2ebb0247a21e14dc6b8
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sun May 22 08:46:39 2016 +1000

guix: ruby-build-system: Extract gemspec during 'extract-gemspec'.

* guix/build/ruby-build-system.scm (build): Move extraction from here ...
(extract-gemspec): ... to here.  New variable.
(first-gemspec): New variable.
(%standard-phases): Add 'extract-gemspec' phase.
---
 guix/build/ruby-build-system.scm |   19 +++
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/guix/build/ruby-build-system.scm b/guix/build/ruby-build-system.scm
index a4ac3b3..79ac380 100644
--- a/guix/build/ruby-build-system.scm
+++ b/guix/build/ruby-build-system.scm
@@ -66,14 +66,13 @@ directory."
   ;; Use GNU unpack strategy for things that aren't gem archives.
   (gnu:unpack #:source source)))
 
-(define* (build #:key source #:allow-other-keys)
-  "Build a new gem using the gemspec from the SOURCE gem."
-  (define (first-gemspec)
-(first-matching-file "\\.gemspec$"))
+(define (first-gemspec)
+  (first-matching-file "\\.gemspec$"))
 
-  ;; Remove the original gemspec, if present, and replace it with a new one.
-  ;; This avoids issues with upstream gemspecs requiring tools such as git to
-  ;; generate the files list.
+(define* (extract-gemspec #:key source #:allow-other-keys)
+  "Remove the original gemspec, if present, and replace it with a new one.
+This avoids issues with upstream gemspecs requiring tools such as git to
+generate the files list."
   (when (gem-archive? source)
 (let ((gemspec (or (false-if-exception (first-gemspec))
;; Make new gemspec if one wasn't shipped.
@@ -94,7 +93,10 @@ directory."
   (write-char (read-char pipe) out
 #t)
   (lambda ()
-(close-pipe pipe))
+(close-pipe pipe)))
+
+(define* (build #:key source #:allow-other-keys)
+  "Build a new gem using the gemspec from the SOURCE gem."
 
   ;; Build a new gem from the current working directory.  This also allows any
   ;; dynamic patching done in previous phases to be present in the installed
@@ -134,6 +136,7 @@ GEM-FLAGS are passed to the 'gem' invokation, if present."
 (define %standard-phases
   (modify-phases gnu:%standard-phases
 (delete 'configure)
+(add-before 'build 'extract-gemspec extract-gemspec)
 (replace 'build build)
 (replace 'unpack unpack)
 (replace 'install install)

08/10: gnu: Add ruby-sequel.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit cbdd428cf4aab436e3080423622c2c2d8fdb84cd
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed May 25 22:08:36 2016 +1000

gnu: Add ruby-sequel.

* gnu/packages/ruby.scm (ruby-sequel): New variable.
---
 gnu/packages/ruby.scm |   22 ++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index afdcb33..f46116e 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3877,3 +3877,25 @@ part of the Prawn PDF generator.")
 ;; From the README: "Matz's terms for Ruby, GPLv2, or GPLv3. See LICENSE
 ;; for details."
 (license (list license:gpl2 license:gpl3 license:ruby
+
+(define-public ruby-sequel
+  (package
+(name "ruby-sequel")
+(version "4.34.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "sequel" version))
+   (sha256
+(base32
+ "0qscddpfwcajggxvbm4a4jv8kkpn6q056bgdg03km34bz8bis1x1"
+(build-system ruby-build-system)
+(arguments
+ '(#:tests? #f)) ; Avoid dependency loop with ruby-minitest-hooks.
+(synopsis "Database toolkit for Ruby")
+(description "Sequel provides thread safety, connection pooling and a
+concise DSL for constructing SQL queries and table schemas.  It includes a
+comprehensive ORM layer for mapping records to Ruby objects and handling
+associated records.")
+(home-page "http://sequel.jeremyevans.net;)
+(license license:expat)))

branch master updated (2301195 -> 803bcc8)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  2301195   gnu: linux-libre: Update to 4.6.
   new  25c288c   guix: ruby-build-system: Extract gemspec during 
'extract-gemspec'.
   new  5e7f1b0   gnu: ruby-nokogiri: Update to 1.6.7.2.
   new  33a45ed   gnu: ruby-domain-name: Update to 0.5.20160310.
   new  80756fa   gnu: ruby-shoulda-matchers: Update to 3.1.1.
   new  0907bf5   gnu: ruby-mime-types-data: Update to 3.2016.0221.
   new  59884b7   gnu: ruby-mini-portile-2: Update to 2.1.0.
   new  f1ae7c6   gnu: ruby-nokogumbo: Update to 1.4.7-1.
   new  cbdd428   gnu: Add ruby-sequel.
   new  2a96dbe   gnu: Add ruby-minitest-hooks.
   new  803bcc8   gnu: ruby-mime-types: Update to 3.1.

The 10 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/ruby.scm|  213 +++---
 guix/build/ruby-build-system.scm |   19 ++--
 2 files changed, 142 insertions(+), 90 deletions(-)

03/10: gnu: ruby-domain-name: Update to 0.5.20160310.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 33a45ed652dbbc8f4f2497a2678bf10b0934efc2
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat May 21 22:57:07 2016 +1000

gnu: ruby-domain-name: Update to 0.5.20160310.

* gnu/packages/ruby.scm (ruby-domain-name): Update to 0.5.20160310.
---
 gnu/packages/ruby.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index b9e8cae..1bd3e93 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3386,14 +3386,14 @@ support to both Ruby and JRuby.  It uses @code{unf_ext} 
on CRuby and
 (define-public ruby-domain-name
   (package
 (name "ruby-domain-name")
-(version "0.5.25")
+(version "0.5.20160310")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "domain_name" version))
(sha256
 (base32
- "16qvfrmcwlzz073aas55mpw2nhyhjcn96s524w0g1wlml242hjav"
+ "0g1175zspkqhlvl9s11g7p2nbmqpvpxxv02q8csd0ryc81laapys"
 (build-system ruby-build-system)
 (arguments
  `(#:phases

02/10: gnu: ruby-nokogiri: Update to 1.6.7.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 5e7f1b0b2a7fc1ac10f61057dfbb828979a4aade
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sun May 22 08:49:41 2016 +1000

gnu: ruby-nokogiri: Update to 1.6.7.2.

* gnu/packages/ruby.scm (ruby-nokogiri): Update to 1.6.7.2.
[arguments]: Relax 'mini_portile2' dependency.
---
 gnu/packages/ruby.scm |   12 +---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 6c2e08f..b9e8cae 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1882,13 +1882,13 @@ to reproduce user environments.")
 (define-public ruby-nokogiri
   (package
 (name "ruby-nokogiri")
-(version "1.6.7.1")
+(version "1.6.7.2")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "nokogiri" version))
   (sha256
(base32
-"12nwv3lad5k2k73aa1d1xy4x577c143ixks6rs70yp78sinbglk2"
+"11sbmpy60ynak6s3794q32lc99hs448msjy8rkp84ay7mq7zqspv"
 (build-system ruby-build-system)
 (arguments
  ;; Tests fail because Nokogiri can only test with an installed extension,
@@ -1897,7 +1897,13 @@ to reproduce user environments.")
#:gem-flags (list "--" "--use-system-libraries"
  (string-append "--with-xml2-include="
 (assoc-ref %build-inputs "libxml2")
-"/include/libxml2" 
+"/include/libxml2" ))
+   #:phases
+   (modify-phases %standard-phases
+ (add-after 'extract-gemspec 'update-dependency
+   (lambda _
+ (substitute* ".gemspec" (("2.0.0.rc2") "2.0"))
+ #t)
 (native-inputs
  `(("ruby-hoe" ,ruby-hoe)
("ruby-rake-compiler" ,ruby-rake-compiler)))

05/10: gnu: ruby-mime-types-data: Update to 3.2016.0221.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 0907bf571dba0f3454362c46b99ace9d0adb0963
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat May 21 23:03:47 2016 +1000

gnu: ruby-mime-types-data: Update to 3.2016.0221.

* gnu/packages/ruby.scm (ruby-mime-types-data): Update to 3.2016.0221.
---
 gnu/packages/ruby.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 8f43ec6..de858fb 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3135,14 +3135,14 @@ that TURN is no longer being maintained.")
 (define-public ruby-mime-types-data
   (package
 (name "ruby-mime-types-data")
-(version "3.2015.1120")
+(version "3.2016.0221")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "mime-types-data" version))
(sha256
 (base32
- "04fzvy02w8d0rrsg8avncn7h58pvwdxj82aps54srb3sam2dkhic"
+ "05ygjn0nnfh6yp1wsi574jckk95wqg9a6g598wk4svvrkmkrzkpn"
 (build-system ruby-build-system)
 (native-inputs
  `(("ruby-hoe" ,ruby-hoe)))

07/10: gnu: ruby-nokogumbo: Update to 1.4.7-1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit f1ae7c6218d6b9d74dbb0ff53e1615290e2ecc96
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat May 21 23:31:56 2016 +1000

gnu: ruby-nokogumbo: Update to 1.4.7-1.

* gnu/packages/ruby.scm (ruby-nokogumbo): Update to 1.4.7-1.
---
 gnu/packages/ruby.scm |  121 +
 1 file changed, 61 insertions(+), 60 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 5c52e32..afdcb33 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2511,67 +2511,68 @@ multibyte strings, internationalization, time zones, 
and testing.")
 (license license:expat)))
 
 (define-public ruby-nokogumbo
-  (package
-(name "ruby-nokogumbo")
-(version "1.4.6")
-(source (origin
-  ;; We use the git reference, because there's no Rakefile in the
-  ;; published gem and the tarball on Github is outdated.
-  (method git-fetch)
-  (uri (git-reference
-(url "https://github.com/rubys/nokogumbo.git;)
-(commit "d56f954d20a")))
-  (file-name (string-append name "-" version "-checkout"))
-  (sha256
-   (base32
-"0bnppjy96xiadrsrc9dp8y6wvdwnkfa930n7acrp0mqm4qywl2wl"
-(build-system ruby-build-system)
-(arguments
- `(#:modules ((guix build ruby-build-system)
-  (guix build utils)
-  (ice-9 rdelim))
-   #:phases
-   (modify-phases %standard-phases
- (add-before 'build 'build-gemspec
-  (lambda _
-(substitute* "Rakefile"
-  ;; Build Makefile even without a copy of gumbo-parser sources
-  (("'gumbo-parser/src',") "")
-  ;; We don't bundle gumbo-parser sources
-  (("'gumbo-parser/src/\\*',") "")
-  (("'gumbo-parser/visualc/include/\\*',") "")
-  ;; The definition of SOURCES will be cut in gemspec, and
-  ;; "FileList" will be undefined.
-  (("SOURCES \\+ FileList\\[")
-   "['ext/nokogumboc/extconf.rb', 'ext/nokogumboc/nokogumbo.c', "))
-
-;; Copy the Rakefile and cut out the gemspec.
-(copy-file "Rakefile" ".gemspec")
-(with-atomic-file-replacement ".gemspec"
-  (lambda (in out)
-(let loop ((line (read-line in 'concat))
-   (skipping? #t))
-  (if (eof-object? line)
-  #t
-  (let ((skip-next? (if skipping?
-(not (string-prefix? "SPEC =" 
line))
-(string-prefix? "end" line
-(when (or (not skipping?)
-  (and skipping? (not skip-next?)))
-  (format #t "~a" line)
-  (display line out))
-(loop (read-line in 'concat) skip-next?))
-#t)
-(inputs
- `(("gumbo-parser" ,gumbo-parser)))
-(propagated-inputs
- `(("ruby-nokogiri" ,ruby-nokogiri)))
-(synopsis "Ruby bindings to the Gumbo HTML5 parser")
-(description
- "Nokogumbo allows a Ruby program to invoke the Gumbo HTML5 parser and
+  (let ((commit "fb51ff299a1c34346837580b6d1d9a60fadf5dbd"))
+(package
+  (name "ruby-nokogumbo")
+  (version (string-append "1.4.7-1." (string-take commit 8)))
+  (source (origin
+;; We use the git reference, because there's no Rakefile in the
+;; published gem and the tarball on Github is outdated.
+(method git-fetch)
+(uri (git-reference
+  (url "https://github.com/rubys/nokogumbo.git;)
+  (commit "d56f954d20a")))
+(file-name (string-append name "-" version "-checkout"))
+(sha256
+ (base32
+  "0bnppjy96xiadrsrc9dp8y6wvdwnkfa930n7acrp0mqm4qywl2wl"
+  (build-system ruby-build-system)
+  (arguments
+   `(#:modules ((guix build ruby-build-system)
+(guix build utils)
+(ice-9 rdelim))
+ #:phases
+ (modify-phases %standard-phases
+   (add-before 'build 'build-gemspec
+(lambda _
+  (substitute* "Rakefile"
+;; Build Makefile even without a copy of gumbo-parser sources
+(("'gumbo-parser/src',") ""

10/10: gnu: ruby-mime-types: Update to 3.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 803bcc81e21b0c2465ca20db59258121fd08a006
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed May 25 21:42:05 2016 +1000

gnu: ruby-mime-types: Update to 3.1.

* gnu/packages/ruby.scm (ruby-mime-types): Update to 3.1.
[native-inputs]: Add 'ruby-minitest-hooks'.
---
 gnu/packages/ruby.scm |7 ---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 631a1cd..6eebd9a 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3187,14 +3187,14 @@ look up the likely MIME type definitions.")
 (define-public ruby-mime-types
   (package
 (name "ruby-mime-types")
-(version "3.0")
+(version "3.1")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "mime-types" version))
(sha256
 (base32
- "1snjc38a9vqvy8j41xld1i1byq9prbl955pbjw7dxqcfcirqlzra"
+ "0087z9kbnlqhci7fxh9f6il63hj1k02icq2rs0c6cppmqchr753m"
 (build-system ruby-build-system)
 (propagated-inputs
  `(("ruby-mime-types-data" ,ruby-mime-types-data)))
@@ -3203,7 +3203,8 @@ look up the likely MIME type definitions.")
("ruby-fivemat" ,ruby-fivemat)
("ruby-minitest-focus" ,ruby-minitest-focus)
("ruby-minitest-rg" ,ruby-minitest-rg)
-   ("ruby-minitest-bonus-assertions" ,ruby-minitest-bonus-assertions)))
+   ("ruby-minitest-bonus-assertions" ,ruby-minitest-bonus-assertions)
+   ("ruby-minitest-hooks" ,ruby-minitest-hooks)))
 (synopsis "Library and registry for MIME content type definitions")
 (description "The mime-types library provides a library and registry for
 information about Multipurpose Internet Mail Extensions (MIME) content type

09/10: gnu: Add ruby-minitest-hooks.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 2a96dbe6d6e49d339e54c4afd3d171712e772311
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed May 25 22:15:13 2016 +1000

gnu: Add ruby-minitest-hooks.

* gnu/packages/ruby.scm (ruby-minitest-hooks): New variable.
---
 gnu/packages/ruby.scm |   27 +++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index f46116e..631a1cd 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1707,6 +1707,33 @@ instance, it provides @code{assert_true}, 
@code{assert_false} and
 (home-page "http://blowmage.com/minitest-rg;)
 (license license:expat)))
 
+(define-public ruby-minitest-hooks
+  (package
+(name "ruby-minitest-hooks")
+(version "1.4.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "minitest-hooks" version))
+   (sha256
+(base32
+ "092fymh0c09v3a585qw3hc15b0zf159s74rxx1ga87drk5jr958z"
+(build-system ruby-build-system)
+(arguments
+ '(#:test-target "spec"))
+(native-inputs
+ `(("ruby-sequel" ,ruby-sequel)
+   ("ruby-sqlite3" ,ruby-sqlite3)))
+(synopsis "Hooks for the minitest framework")
+(description
+ "Minitest-hooks adds @code{around}, @code{before_all}, @code{after_all},
+@code{around_all} hooks for Minitest.  This allows, for instance, running each
+suite of specs inside a database transaction, running each spec inside its own
+savepoint inside that transaction.  This can significantly speed up testing
+for specs that share expensive database setup code.")
+(home-page "http://github.com/jeremyevans/minitest-hooks;)
+(license license:expat)))
+
 (define-public ruby-daemons
   (package
 (name "ruby-daemons")

branch master updated (3c47489 -> 88bb419)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  3c47489   gnu: Add gnome-calendar.
   new  88bb419   gnu: Add python2-rope.

The 1 revisions listed above as "new" are entirely new to this
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been added to this reference.


Summary of changes:
 gnu/packages/python.scm |   28 
 1 file changed, 28 insertions(+)

01/01: gnu: Add python2-rope.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 88bb4197c419d6095cc4061bac1ee0f96bf939b1
Author: Lukas Gradl 
Date:   Sat May 21 18:19:42 2016 -0500

gnu: Add python2-rope.

* gnu/packages/python.scm (python2-rope): New variable.
---
 gnu/packages/python.scm |   28 
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 37c8594..602da2d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -18,6 +18,7 @@
 ;;; Copyright © 2015 Kyle Meyer 
 ;;; Copyright © 2015, 2016 Chris Marusich 
 ;;; Copyright © 2016 Danny Milosavljevic 
+;;; Copyright © 2016 Lukas Gradl 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -8760,3 +8761,30 @@ respectively.")
   (description (string-append "This is an experimental compiler for a subset of
 Python.  It generates C++ code and a Makefile."))
   (license (list gpl3 bsd-3 license:expat
+
+(define-public python2-rope
+  (package
+(name "python2-rope")
+(version "0.10.3")
+(source
+ (origin
+  (method url-fetch)
+  (uri (pypi-uri "rope" version))
+  (sha256
+(base32
+ "18k5znhpwvrfck3yp0jmhd5j8r0f0s8bk1zh5yhs2cfgmfhbwigb"
+(arguments
+ ;; Rope is currently python-2 only.
+ ;; https://github.com/python-rope/rope/issues/57
+ `(#:python ,python-2))
+(build-system python-build-system)
+(native-inputs
+ `(("python2-unittest2" ,python2-unittest2)
+   ("python2-setuptools" ,python2-setuptools)))
+(home-page "https://github.com/python-rope/rope;)
+(synopsis "Refactoring library for Python")
+(description "Rope is a refactoring library for Python.  It facilitates
+the renaming, moving and extracting of attributes, functions, modules, fields
+and parameters in Python 2 source code.  These refactorings can also be applied
+to occurences in strings and comments.")
+(license gpl2)))

01/01: gnu: Add r-biased-urn.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 0947698c42fb10b8802679cbc58f9a42a2d91043
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed May 18 21:47:35 2016 +1000

gnu: Add r-biased-urn.

* gnu/packages/statistics.scm (r-biased-urn): New variable.
---
 gnu/packages/statistics.scm |   23 +++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7b34832..58f5c9d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efr...@flashner.co.il>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.g...@thebird.nl>
 ;;; Copyright © 2016 Roel Janssen <r...@gnu.org>
+;;; Copyright © 2016 Ben Woodcroft <donttrust...@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2593,6 +2594,28 @@ directly from R.  Once uploaded to a plotly account, 
plotly graphs (and the
 data behind them) can be viewed and modified in a web browser.")
 (license license:x11)))
 
+(define-public r-biased-urn
+  (package
+   (name "r-biased-urn")
+   (version "1.07")
+   (source
+(origin
+ (method url-fetch)
+ (uri (cran-uri "BiasedUrn" version))
+ (sha256
+  (base32
+   "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"
+   (properties `((upstream-name . "BiasedUrn")))
+   (build-system r-build-system)
+   (home-page "http://www.agner.org/random/;)
+   (synopsis "Biased urn model distributions")
+   (description
+"This package provides statistical models of biased sampling in the form
+of univariate and multivariate noncentral hypergeometric distributions,
+including Wallenius' noncentral hypergeometric distribution and Fisher's
+noncentral hypergeometric distribution (also called extended hypergeometric
+distribution).")
+   (license license:gpl3+)))
 
 (define-public r-ztable
   (package

branch master updated (44c5f02 -> 0947698)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  44c5f02   gnu: giflib: Use 'modify-phases'.
   new  0947698   gnu: Add r-biased-urn.

The 1 revisions listed above as "new" are entirely new to this
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been added to this reference.


Summary of changes:
 gnu/packages/statistics.scm |   23 +++
 1 file changed, 23 insertions(+)

branch master updated (0affdfb -> bd9fe0f)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  0affdfb   gnu: hurd-headers: Update to 0.8.
   new  bd9fe0f   gnu: Add krona-tools.

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Summary of changes:
 gnu/packages/web.scm |   96 ++
 1 file changed, 96 insertions(+)

01/01: gnu: diamond: Do not specify target architecture.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 7c544991dcee6cf8f79484f12a8249ede38d2dd2
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed May 18 21:21:09 2016 +1000

gnu: diamond: Do not specify target architecture.

* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not
specify target architecture.
---
 gnu/packages/bioinformatics.scm |8 +++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f79728..8cec840 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1494,7 +1494,13 @@ identify enrichments with functional annotations of the 
genome.")
 "1dqancz32c2l7w1b2vkvh5zqa2jnf99j1c41djnx1l8pxn044zdc"
 (build-system cmake-build-system)
 (arguments
- '(#:tests? #f)) ; no "check" target
+ '(#:tests? #f ; no "check" target
+   #:phases
+   (modify-phases %standard-phases
+ (add-after 'unpack 'remove-native-compilation
+   (lambda _
+ (substitute* "CMakeLists.txt" (("-march=native") ""))
+ #t)
 (inputs
  `(("zlib" ,zlib)))
 (home-page "https://github.com/bbuchfink/diamond;)

branch master updated (e62ffce -> 7c54499)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  e62ffce   gnu: Add Piranha.
   new  7c54499   gnu: diamond: Do not specify target architecture.

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 gnu/packages/bioinformatics.scm |8 +++-
 1 file changed, 7 insertions(+), 1 deletion(-)

branch master updated (122395f -> 849485f)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  122395f   gnu: diamond: Update to 0.8.1.
   new  daaeed7   gnu: vsearch: Update to 1.11.1.
   new  849485f   gnu: sortmerna: Update to 2.1b.

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Summary of changes:
 gnu/packages/bioinformatics.scm |   10 ++
 1 file changed, 6 insertions(+), 4 deletions(-)

02/02: gnu: sortmerna: Update to 2.1b.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 849485f5a05badf502e28c673e546b4660c4ca46
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue May 17 21:45:49 2016 +1000

gnu: sortmerna: Update to 2.1b.

* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
---
 gnu/packages/bioinformatics.scm |6 --
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7aa1853..60cf6b7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3549,7 +3549,7 @@ of these reads to align data quickly through a hash-based 
indexing scheme.")
 (define-public sortmerna
   (package
 (name "sortmerna")
-(version "2.1")
+(version "2.1b")
 (source
  (origin
(method url-fetch)
@@ -3559,7 +3559,7 @@ of these reads to align data quickly through a hash-based 
indexing scheme.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1mc5cf1c7xh0h7xb11vh7gqgzx0qvrfa606cb8ixlfg3f2av58s4"
+ "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"
 (build-system gnu-build-system)
 (outputs '("out"  ;for binaries
"db")) ;for sequence databases
@@ -3579,6 +3579,8 @@ of these reads to align data quickly through a hash-based 
indexing scheme.")
(install-file file share))
  (find-files "rRNA_databases" ".*fasta"))
#t))
+(inputs
+ `(("zlib" ,zlib)))
 (home-page "http://bioinfo.lifl.fr/RNA/sortmerna;)
 (synopsis "Biological sequence analysis tool for NGS reads")
 (description

01/02: gnu: vsearch: Update to 1.11.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit daaeed765aebae138b4af1d3861eace0368fe2a6
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue May 17 21:36:46 2016 +1000

gnu: vsearch: Update to 1.11.1.

* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
---
 gnu/packages/bioinformatics.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f882185..7aa1853 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3810,7 +3810,7 @@ data in the form of VCF files.")
 (define-public vsearch
   (package
 (name "vsearch")
-(version "1.10.0")
+(version "1.11.1")
 (source
  (origin
(method url-fetch)
@@ -3820,7 +3820,7 @@ data in the form of VCF files.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1i3bad7gnn2y3a1yfixzshd99xdkjc8w5bxzgifpysc6jiljwvb5"))
+ "1pdvm3znjgq3zryy240yj9gc0bf1z31k6vf9jxrxgdgkvzgw85c7"))
(modules '((guix build utils)))
(snippet
 '(begin

branch master updated (a9e41d2 -> 122395f)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  a9e41d2   gnu: emacs-constants: Factorize home-page in source URL.
   new  122395f   gnu: diamond: Update to 0.8.1.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |   31 +--
 1 file changed, 5 insertions(+), 26 deletions(-)

01/01: gnu: diamond: Update to 0.8.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 122395f9fc42de7dbe2643b437ca4e484adb8ba0
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue May 17 21:07:00 2016 +1000

gnu: diamond: Update to 0.8.1.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
---
 gnu/packages/bioinformatics.scm |   31 +--
 1 file changed, 5 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa16d39..f882185 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1482,7 +1482,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.7.9")
+(version "0.8.1")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -1491,33 +1491,12 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
-  (snippet '(begin
-  (delete-file "bin/diamond")
-  #t
-(build-system gnu-build-system)
+"1dqancz32c2l7w1b2vkvh5zqa2jnf99j1c41djnx1l8pxn044zdc"
+(build-system cmake-build-system)
 (arguments
- '(#:tests? #f  ;no "check" target
-   #:phases
-   (modify-phases %standard-phases
- (add-after 'unpack 'enter-source-dir
-(lambda _
-  (chdir "src")
-  #t))
- (delete 'configure)
- (replace 'install
-  (lambda* (#:key outputs #:allow-other-keys)
-(let ((bin (string-append (assoc-ref outputs "out")
-  "/bin")))
-  (mkdir-p bin)
-  (copy-file "../bin/diamond"
- (string-append bin "/diamond"))
-  #t))
-(native-inputs
- `(("bc" ,bc)))
+ '(#:tests? #f)) ; no "check" target
 (inputs
- `(("boost" ,boost)
-   ("zlib" ,zlib)))
+ `(("zlib" ,zlib)))
 (home-page "https://github.com/bbuchfink/diamond;)
 (synopsis "Accelerated BLAST compatible local sequence aligner")
 (description

01/01: gnu: ruby-hashery: Update to 2.1.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit cba962086da190b474df4f55bf2b50278f519640
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Mon May 2 10:20:17 2016 +1000

gnu: ruby-hashery: Update to 2.1.2.

* gnu/packages/ruby.scm (ruby-hashery): Update to 2.1.2.
[arguments]: Remove test workaround.
---
 gnu/packages/ruby.scm |8 ++--
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 2aab8bf..6c2e08f 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3737,24 +3737,20 @@ Rubytest-based test frameworks.  It provides the 
@code{rubytest} executable.")
 (define-public ruby-hashery
   (package
 (name "ruby-hashery")
-(version "2.1.1")
+(version "2.1.2")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "hashery" version))
(sha256
 (base32
- "0xawbljsjarl9l7700bka672ixwznzwih4s9i38p1y9mp8hyx54g"
+ "0qj8815bf7q6q7llm5rzdz279gzmpqmqqicxnzv066a020iwqffj"
 (build-system ruby-build-system)
 (arguments
  `(#:phases
(modify-phases %standard-phases
  (replace 'check
(lambda _
- ;; Remove known test failure documented at
- ;; https://github.com/rubyworks/hashery/issues/25
- (substitute* "test/case_key_hash.rb"
-   (("^  assert\\(s\\)") ""))
  (and (zero? (system* "qed"))
   (zero? (system* "rubytest" "-Ilib" "-Itest" "test/"
 (native-inputs

branch master updated (ae4ff9f -> cba9620)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  ae4ff9f   syscalls: Add 'tcgetattr' and 'tcsetattr' bindings.
   new  cba9620   gnu: ruby-hashery: Update to 2.1.2.

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 gnu/packages/ruby.scm |8 ++--
 1 file changed, 2 insertions(+), 6 deletions(-)

branch master updated (6c0e2db -> 324efb8)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  6c0e2db   gnu: subversion: Update to 1.8.16 [fixes 
CVE-2016-{2167,2168}].
   new  324efb8   gnu: Add muscle.

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 gnu/packages/bioinformatics.scm |   35 +++
 1 file changed, 35 insertions(+)

01/01: gnu: Add muscle.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 324efb0834bbe9bb55387b63dafd600e93e9
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat Jan 16 22:12:23 2016 +1000

gnu: Add muscle.

* gnu/packages/bioinformatics.scm (muscle): New variable.
---
 gnu/packages/bioinformatics.scm |   35 +++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 620439f..079fd46 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2548,6 +2548,41 @@ RNA-Seq, the MISO model uses Bayesian inference to 
compute the probability
 that a read originated from a particular isoform.")
 (license license:gpl2)))
 
+(define-public muscle
+  (package
+(name "muscle")
+(version "3.8.1551")
+(source (origin
+  (method url-fetch/tarbomb)
+  (file-name (string-append name "-" version))
+  (uri (string-append
+"http://www.drive5.com/muscle/muscle_src_;
+version ".tar.gz"))
+  (sha256
+   (base32
+"0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"
+(build-system gnu-build-system)
+(arguments
+ `(#:make-flags (list "LDLIBS = -lm")
+   #:phases
+   (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'check
+   ;; There are no tests, so just test if it runs.
+   (lambda _ (zero? (system* "./muscle" "-version"
+ (replace 'install
+   (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+(bin (string-append out "/bin")))
+   (install-file "muscle" bin)))
+(home-page "http://www.drive5.com/muscle;)
+(synopsis "Multiple sequence alignment program")
+(description
+ "MUSCLE aims to be a fast and accurate multiple sequence alignment
+program for nucleotide and protein sequences.")
+;; License information found in 'muscle -h' and usage.cpp.
+(license license:public-domain)))
+
 (define-public orfm
   (package
 (name "orfm")

01/02: gnu: ruby: Update to 2.3.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit b0e52f52b76ecc37a9b6469e6f72c4b4757979ce
Author: Rob Syme 
Date:   Sat Apr 30 08:39:27 2016 +1000

gnu: ruby: Update to 2.3.1.

* gnu/packages/ruby.scm (ruby): Update to 2.3.1.
[origin] Add symlink patch.
* gnu/packages/patches/ruby-symlinkfix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add patch.
---
 gnu/local.mk   |1 +
 gnu/packages/patches/ruby-symlinkfix.patch |   53 
 gnu/packages/ruby.scm  |5 +--
 3 files changed, 57 insertions(+), 2 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 9308c38..7556fa7 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -723,6 +723,7 @@ dist_patch_DATA =   
\
   gnu/packages/patches/readline-link-ncurses.patch \
   gnu/packages/patches/ripperx-missing-file.patch  \
   gnu/packages/patches/rsem-makefile.patch \
+  gnu/packages/patches/ruby-symlinkfix.patch\
   gnu/packages/patches/sed-hurd-path-max.patch \
   gnu/packages/patches/scheme48-tests.patch\
   gnu/packages/patches/scotch-test-threading.patch \
diff --git a/gnu/packages/patches/ruby-symlinkfix.patch 
b/gnu/packages/patches/ruby-symlinkfix.patch
new file mode 100644
index 000..16beecc
--- /dev/null
+++ b/gnu/packages/patches/ruby-symlinkfix.patch
@@ -0,0 +1,53 @@
+Fix symlinks to '..' to fix rubygems improperly expanding symlinked
+paths. Without this fix, some gems fail to install. This patch is applied in
+rubygems 2.5.2, but ruby version 2.3.1 bundles an older version of rubygems
+(2.5.1).
+
+--- a/lib/rubygems/package.rb
 b/lib/rubygems/package.rb
+@@ -383,7 +383,7 @@ def extract_tar_gz io, destination_dir, pattern = "*" # 
:nodoc:
+   FileUtils.chmod entry.header.mode, destination
+ end if entry.file?
+
+-File.symlink(install_location(entry.header.linkname, 
destination_dir), destination) if entry.symlink?
++File.symlink(entry.header.linkname, destination) if entry.symlink?
+
+ verbose destination
+   end
+diff --git a/test/rubygems/test_gem_package.rb 
b/test/rubygems/test_gem_package.rb
+index 7848bc2..f287bd3 100644
+--- a/test/rubygems/test_gem_package.rb
 b/test/rubygems/test_gem_package.rb
+@@ -428,19 +428,25 @@ def test_extract_tar_gz_absolute
+  "#{@destination} is not allowed", e.message)
+   end
+
+-  def test_extract_tar_gz_symlink_absolute
++  def test_extract_tar_gz_symlink_relative_path
++skip 'symlink not supported' if Gem.win_platform?
++
+ package = Gem::Package.new @gem
+
+ tgz_io = util_tar_gz do |tar|
+-  tar.add_symlink 'code.rb', '/absolute.rb', 0644
++  tar.add_file'relative.rb', 0644 do |io| io.write 'hi' end
++  tar.mkdir   'lib', 0755
++  tar.add_symlink 'lib/foo.rb', '../relative.rb', 0644
+ end
+
+-e = assert_raises Gem::Package::PathError do
+-  package.extract_tar_gz tgz_io, @destination
+-end
++package.extract_tar_gz tgz_io, @destination
+
+-assert_equal("installing into parent path /absolute.rb of " +
+- "#{@destination} is not allowed", e.message)
++extracted = File.join @destination, 'lib/foo.rb'
++assert_path_exists extracted
++assert_equal '../relative.rb',
++ File.readlink(extracted)
++assert_equal 'hi',
++ File.read(extracted)
+   end
+
+   def test_extract_tar_gz_directory
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index bafa7e3..b8a6d01 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -46,7 +46,7 @@
 (define-public ruby
   (package
 (name "ruby")
-(version "2.3.0")
+(version "2.3.1")
 (source
  (origin
(method url-fetch)
@@ -55,8 +55,9 @@
"/ruby-" version ".tar.xz"))
(sha256
 (base32
- "15s0dsb5ynf3d2w5gzawnszq5594fqvapv2y7a0qw16przq5l4kh"))
+ "0f3395q7pd2hrl2gv26bib80038sjawxgmhl9zn22fjs9m9va9b7"))
(modules '((guix build utils)))
+   (patches (search-patches "ruby-symlinkfix.patch"))
(snippet `(begin
;; Remove bundled libffi
(delete-file-recursively

branch master updated (f36a1eb -> 9d17702)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  f36a1eb   gnu: Add Fossil.
   new  b0e52f5   gnu: ruby: Update to 2.3.1.
   new  9d17702   gnu: ruby-hashery: Disable failing test.

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Summary of changes:
 gnu/local.mk   |1 +
 gnu/packages/patches/ruby-symlinkfix.patch |   53 
 gnu/packages/ruby.scm  |9 +++--
 3 files changed, 61 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/ruby-symlinkfix.patch

02/02: gnu: ruby-hashery: Disable failing test.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 9d177025005a2bcae50c698d0363fd4096d50157
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat Apr 30 08:44:57 2016 +1000

gnu: ruby-hashery: Disable failing test.

* gnu/packages/ruby.scm (ruby-hashery)[arguments]: Remove failing
test.
---
 gnu/packages/ruby.scm |4 
 1 file changed, 4 insertions(+)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index b8a6d01..2aab8bf 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3751,6 +3751,10 @@ Rubytest-based test frameworks.  It provides the 
@code{rubytest} executable.")
(modify-phases %standard-phases
  (replace 'check
(lambda _
+ ;; Remove known test failure documented at
+ ;; https://github.com/rubyworks/hashery/issues/25
+ (substitute* "test/case_key_hash.rb"
+   (("^  assert\\(s\\)") ""))
  (and (zero? (system* "qed"))
   (zero? (system* "rubytest" "-Ilib" "-Itest" "test/"
 (native-inputs

01/01: gnu: ruby-2.2: Update to 2.2.5.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 416381daa2f73a06a7af324032413d9de46bbfb3
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed Apr 27 17:39:05 2016 +1000

gnu: ruby-2.2: Update to 2.2.5.

* gnu/packages/ruby.scm (ruby-2.2): Update to 2.2.5.
[origin]: Remove snippet.
---
 gnu/packages/ruby.scm |   10 ++
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 8531b9c..bafa7e3 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -102,7 +102,7 @@ a focus on simplicity and productivity.")
 
 (define-public ruby-2.2
   (package (inherit ruby)
-(version "2.2.4")
+(version "2.2.5")
 (source
  (origin
(method url-fetch)
@@ -111,13 +111,7 @@ a focus on simplicity and productivity.")
"/ruby-" version ".tar.xz"))
(sha256
 (base32
- "0g3ps4q3iz7wj9m45n8xyxzw8nh29ljdqb87b0f6i0p3853gz2yj"))
-   (modules '((guix build utils)))
-   (snippet `(begin
-   ;; Remove bundled libffi
-   (delete-file-recursively
-(string-append "ext/fiddle/libffi-3.2.1"))
-   #t))
+ "1mw7bzw76g5w37cwhb57r6gxcl2vn9lfrlyf4h4xms3qlnhflvzq"))
 
 (define-public ruby-2.1
   (package (inherit ruby)

branch master updated (8e740bc -> 416381d)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  8e740bc   gnu: icedtea-8: Update to 3.0.1.
   new  416381d   gnu: ruby-2.2: Update to 2.2.5.

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been added to this reference.


Summary of changes:
 gnu/packages/ruby.scm |   10 ++
 1 file changed, 2 insertions(+), 8 deletions(-)

branch master updated (e969b14 -> 79b555e)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  e969b14   Revert "Merge branch 'gnome-updates'"
   new  79b555e   gnu: samtools: Update to 1.3.1.

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Summary of changes:
 gnu/packages/bioinformatics.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

01/01: gnu: samtools: Update to 1.3.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 79b555edeb469b4d92ef31b66d9b5961001e1a68
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sun Apr 24 09:45:07 2016 +1000

gnu: samtools: Update to 1.3.1.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.1.
---
 gnu/packages/bioinformatics.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c49b0a9..899ce1c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2902,7 +2902,7 @@ distribution, coverage uniformity, strand specificity, 
etc.")
 (define-public samtools
   (package
 (name "samtools")
-(version "1.3")
+(version "1.3.1")
 (source
  (origin
(method url-fetch)
@@ -2911,7 +2911,7 @@ distribution, coverage uniformity, strand specificity, 
etc.")
version "/samtools-" version ".tar.bz2"))
(sha256
 (base32
- "03mnf0mhbfwhqlqfslrhfnw68s3g0fs1as354i9a584mqw1l1smy"
+ "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc"
 (build-system gnu-build-system)
 (arguments
  `(#:modules ((ice-9 ftw)

branch master updated (ffba7d4 -> 9bb46c1)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  ffba7d4   mapped-devices: LUKS partitions can be designated by 
their UUID.
   new  9bb46c1   gnu: ruby-bio-commandeer: Update to 0.1.3.

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Summary of changes:
 gnu/packages/ruby.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

01/01: gnu: ruby-bio-commandeer: Update to 0.1.3.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 9bb46c155b463029f3da84d1b146efa79785a4ac
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Mon Apr 18 14:58:43 2016 +1000

gnu: ruby-bio-commandeer: Update to 0.1.3.

* gnu/packages/ruby.scm (ruby-bio-commandeer): Update to 0.1.3.
---
 gnu/packages/ruby.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 0ca3415..8531b9c 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3528,14 +3528,14 @@ subprocess.")
 (define-public ruby-bio-commandeer
   (package
 (name "ruby-bio-commandeer")
-(version "0.1.2")
+(version "0.1.3")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "bio-commandeer" version))
(sha256
 (base32
- "061jxa6km92qfwzl058r2gp8gfcsbyr7m643nw1pxvmjdswaf6ly"
+ "0lin6l99ldqqjc90l9ihcrv882c4xgbgqm16jqkdy6jf955jd9a8"
 (build-system ruby-build-system)
 (arguments
  `(#:phases

01/01: gnu: Remove duplicate python-pbr.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e25f017422899c3e43cf42e254f46053bf4c4243
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sun Apr 3 21:09:17 2016 +1000

gnu: Remove duplicate python-pbr.

This is a follow-up to commit 1ef09c0c75c61fd70a84667a845a652995b38a94.

* gnu/packages/openstack.scm (python-pbr, python2-pbr): Move from here ...
* gnu/packages/python.scm: ... to here.
(python-pbr, python2-pbr): Delete duplicate packages.
---
 gnu/packages/openstack.scm |   43 ---
 gnu/packages/python.scm|   48 ---
 2 files changed, 35 insertions(+), 56 deletions(-)

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 0fa488f..947abf3 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -20,7 +20,6 @@
 (define-module (gnu packages openstack)
   #:use-module (gnu packages python)
   #:use-module (gnu packages tls)
-  #:use-module (gnu packages version-control)
   #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module ((guix licenses)
@@ -235,48 +234,6 @@ tested on Python version 3.2, 2.7 and 2.6.")
 (define-public python2-os-testr
   (package-with-python2 python-os-testr))
 
-(define-public python-pbr
-  (package
-(name "python-pbr")
-(version "1.8.1")
-(source
-  (origin
-(method url-fetch)
-(uri (string-append
-   "https://pypi.python.org/packages/source/p/pbr/pbr-;
-   version
-   ".tar.gz"))
-(sha256
-  (base32
-"0jcny36cf3s8ar5r4a575npz080hndnrfs4np1fqhv0ym4k7c4p2"
-(build-system python-build-system)
-(arguments
- `(#:tests? #f)) ;; Most tests seem to use the Internet.
-(propagated-inputs
-  `(("python-testrepository" ,python-testrepository)
-("git" ,git))) ;; pbr actually uses the "git" binary.
-(inputs
-  `(("python-fixtures" ,python-fixtures)
-("python-mimeparse" ,python-mimeparse)
-("python-mock" ,python-mock)
-("python-setuptools" ,python-setuptools)
-("python-six" ,python-six)
-("python-sphinx" ,python-sphinx)
-("python-testrepository" ,python-testrepository)
-("python-testresources" ,python-testresources)
-("python-testscenarios" ,python-testscenarios)
-("python-testtools" ,python-testtools)
-("python-virtualenv" ,python-virtualenv)))
-(home-page "https://launchpad.net/pbr;)
-(synopsis "Change the default behavior of Python’s setuptools")
-(description
-  "Python Build Reasonableness (PBR) is a library that injects some useful
-and sensible default behaviors into your setuptools run.")
-(license asl2.0)))
-
-(define-public python2-pbr
-  (package-with-python2 python-pbr))
-
 (define-public python-requests-mock
   (package
 (name "python-requests-mock")
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 66ed16a..414503f 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -69,6 +69,7 @@
   #:use-module (gnu packages texlive)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages web)
   #:use-module (gnu packages base)
   #:use-module (gnu packages xml)
@@ -1875,25 +1876,46 @@ and sensible default behaviors into your setuptools 
run.")
   (package-with-python2 python-pbr-0.11))
 
 (define-public python-pbr
-  (package (inherit python-pbr-0.11)
+  (package
+(name "python-pbr")
 (version "1.8.1")
 (source
- (origin
-   (method url-fetch)
-   (uri (pypi-uri "pbr" version))
-   (sha256
-(base32
- "0jcny36cf3s8ar5r4a575npz080hndnrfs4np1fqhv0ym4k7c4p2"
+  (origin
+(method url-fetch)
+(uri (string-append
+   "https://pypi.python.org/packages/source/p/pbr/pbr-;
+   version
+   ".tar.gz"))
+(sha256
+  (base32
+"0jcny36cf3s8ar5r4a575npz080hndnrfs4np1fqhv0ym4k7c4p2"
 (build-system python-build-system)
+(arguments
+ `(#:tests? #f)) ;; Most tests seem to use the Internet.
+(propagated-inputs
+  `(("python-testrepository" ,python-testrepository)
+("git" ,git))) ;; pbr actually uses the "git" binary.
 (inputs
- `(("python-setuptools" ,python-setuptools)
-   ("python-fixtures" ,python-fixtures)
-   ("python-pip" ,python-pip)))
-(properties `((python2-variant . ,(delay python2-pbr

branch master updated (692add5 -> e25f017)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  692add5   gnu: python-lockfile: Update to 0.12.2.
   new  e25f017   gnu: Remove duplicate python-pbr.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/openstack.scm |   43 ---
 gnu/packages/python.scm|   48 ---
 2 files changed, 35 insertions(+), 56 deletions(-)

02/04: gnu: Add python-pbr.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 1ef09c0c75c61fd70a84667a845a652995b38a94
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sun Apr 3 15:15:40 2016 +1000

gnu: Add python-pbr.

* gnu/packages/python.scm (python-pbr, python2-pbr): New variables.
---
 gnu/packages/python.scm |   21 +
 1 files changed, 21 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f919808..d79cb13 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1867,6 +1867,27 @@ and sensible default behaviors into your setuptools 
run.")
 (define-public python2-pbr-0.11
   (package-with-python2 python-pbr-0.11))
 
+(define-public python-pbr
+  (package (inherit python-pbr-0.11)
+(version "1.8.1")
+(source
+ (origin
+   (method url-fetch)
+   (uri (pypi-uri "pbr" version))
+   (sha256
+(base32
+ "0jcny36cf3s8ar5r4a575npz080hndnrfs4np1fqhv0ym4k7c4p2"
+(build-system python-build-system)
+(inputs
+ `(("python-setuptools" ,python-setuptools)
+   ("python-fixtures" ,python-fixtures)
+   ("python-pip" ,python-pip)))
+(properties `((python2-variant . ,(delay python2-pbr))
+
+(define-public python2-pbr
+  (package (inherit (package-with-python2
+ (strip-python2-variant python-pbr)
+
 (define-public python-fixtures
   (package
 (name "python-fixtures")

branch master updated (fd7575d -> 692add5)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  fd7575d   gnu: pspp: Update to 0.10.1.
   new  78c0d32   gnu: python-pandas: Update to 0.18.0.
   new  1ef09c0   gnu: Add python-pbr.
   new  1804527   gnu: python-lockfile Use 'python2-variant'.
   new  692add5   gnu: python-lockfile: Update to 0.12.2.

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Summary of changes:
 gnu/packages/python.scm |   46 ++
 1 files changed, 34 insertions(+), 12 deletions(-)

01/01: gnu: ruby-2.1: Update to 2.1.10.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a754eaf16dff20cb0ae7c0ca32f50647f1f2b10e
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat Apr 2 09:16:17 2016 +1000

gnu: ruby-2.1: Update to 2.1.10.

* gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.10.
---
 gnu/packages/ruby.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 2abb261..0ca3415 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -121,7 +121,7 @@ a focus on simplicity and productivity.")
 
 (define-public ruby-2.1
   (package (inherit ruby)
-(version "2.1.8")
+(version "2.1.10")
 (source
  (origin
(method url-fetch)
@@ -130,7 +130,7 @@ a focus on simplicity and productivity.")
"/ruby-" version ".tar.bz2"))
(sha256
 (base32
- "11rkbfc90cg9p9mzg32475alf3ddcn9q8a3ar3fwm5xskic0n395"
+ "1wglbd599mlwxfcb2xgqcxi2shr363pjn5dpbv11m04si9bpaim7"
 (arguments
  `(#:test-target "test"
#:parallel-tests? #f

branch master updated (f044337 -> a754eaf)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  f044337   gnu: glpk: Update to 4.60.
   new  a754eaf   gnu: ruby-2.1: Update to 2.1.10.

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 gnu/packages/ruby.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

01/01: import: Add github-updater.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 917a2a58ec3db94983198c447061a41048cfc6a1
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sun Nov 15 10:18:05 2015 +1000

import: Add github-updater.

* guix/import/github.scm: New file.
* guix/scripts/refresh.scm (%updaters): Add %GITHUB-UPDATER.
* doc/guix.texi (Invoking guix refresh): Mention it.
* Makefile.am (MODULES): Add gnu/import/github.scm.
---
 Makefile.am  |1 +
 doc/guix.texi|   15 
 guix/import/github.scm   |  198 ++
 guix/scripts/refresh.scm |3 +-
 4 files changed, 216 insertions(+), 1 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 01d7fbe..4c53779 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -109,6 +109,7 @@ MODULES =   \
   guix/import/cran.scm \
   guix/import/hackage.scm  \
   guix/import/elpa.scm \
+  guix/import/github.scm   \
   guix/scripts.scm \
   guix/scripts/download.scm\
   guix/scripts/build.scm   \
diff --git a/doc/guix.texi b/doc/guix.texi
index c111b0f..4c9a91b 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -17,6 +17,7 @@ Copyright @copyright{} 2015 Mathieu Lirzin@*
 Copyright @copyright{} 2014 Pierre-Antoine Rault@*
 Copyright @copyright{} 2015 Taylan Ulrich Bayırlı/Kammer@*
 Copyright @copyright{} 2015, 2016 Leo Famulari
+Copyright @copyright{} 2016 Ben Woodcroft
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -4660,6 +4661,8 @@ the updater for @uref{http://www.bioconductor.org/, 
Bioconductor} R packages;
 the updater for @uref{https://pypi.python.org, PyPI} packages.
 @item gem
 the updater for @uref{https://rubygems.org, RubyGems} packages.
+@item github
+the updater for @uref{https://github.com, GitHub} packages.
 @end table
 
 For instance, the following command only checks for updates of Emacs
@@ -4746,6 +4749,18 @@ Use @var{host} as the OpenPGP key server when importing 
a public key.
 
 @end table
 
+The @code{github} updater uses the
+@uref{https://developer.github.com/v3/, GitHub API} to query for new
+releases.  When used repeatedly e.g. when refreshing all packages,
+GitHub will eventually refuse to answer any further API requests.  By
+default 60 API requests per hour are allowed, and a full refresh on all
+GitHub packages in Guix requires more than this.  Authentication with
+GitHub through the use of an API token alleviates these limits.  To use
+an API token, set the environment variable @code{GUIX_GITHUB_TOKEN} to a
+token procured from @uref{https://github.com/settings/tokens} or
+otherwise.
+
+
 @node Invoking guix lint
 @section Invoking @command{guix lint}
 The @command{guix lint} command is meant to help package developers avoid
diff --git a/guix/import/github.scm b/guix/import/github.scm
new file mode 100644
index 000..c696dcb
--- /dev/null
+++ b/guix/import/github.scm
@@ -0,0 +1,198 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Ben Woodcroft <donttrust...@gmail.com>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (guix import github)
+  #:use-module (ice-9 match)
+  #:use-module (srfi srfi-1)
+  #:use-module (json)
+  #:use-module (guix utils)
+  #:use-module ((guix download) #:prefix download:)
+  #:use-module (guix import utils)
+  #:use-module (guix packages)
+  #:use-module (guix upstream)
+  #:use-module (gnu packages)
+  #:use-module (web uri)
+  #:export (%github-updater))
+
+(define (json-fetch* url)
+  "Return a list/hash representation of the JSON resource URL, or #f on
+failure."
+  (call-with-output-file "/dev/null"
+(lambda (null)
+  (with-error-to-port null
+(lambda ()
+  (call-with-temporary-output-file
+   (lambda (temp port)
+ (and (url-fetch url temp)
+  (call-with-input-file temp json->scm)
+
+(define (find-extension url)
+  "Return the extension of the archive e.g. '.tar.gz' given a URL, or
+false if none is recognized"
+  (find (lamb

branch master updated (22572d5 -> 917a2a5)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  22572d5   store: 'path-info-deriver' is #f when there is no deriver.
   new  917a2a5   import: Add github-updater.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 Makefile.am  |1 +
 doc/guix.texi|   15 
 guix/import/github.scm   |  198 ++
 guix/scripts/refresh.scm |3 +-
 4 files changed, 216 insertions(+), 1 deletions(-)
 create mode 100644 guix/import/github.scm

01/01: import: gem: Add updater.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit fbc5b815cce85a6af75226ab16acf243fd7d22ce
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Fri Jan 1 16:56:07 2016 +1000

import: gem: Add updater.

* guix/import/gem.scm (guix-package->gem-name,
  gem-package?, latest-release): New procedures.
  (%gem-updater): New variable.
  (rubygems-fetch): Wrap body in
  'call-with-output-file' and 'with-error-to-port'.
* guix/scripts/refresh.scm (%updaters): Add %GEM-UPDATER.
* doc/guix.texi (Invoking guix refresh): Mention RubyGems.
---
 doc/guix.texi|2 +
 guix/import/gem.scm  |   63 +++--
 guix/scripts/refresh.scm |5 +++-
 3 files changed, 66 insertions(+), 4 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index c5a7de7..b991cc1 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -4571,6 +4571,8 @@ the updater for @uref{http://cran.r-project.org/, CRAN} 
packages;
 the updater for @uref{http://www.bioconductor.org/, Bioconductor} R packages;
 @item pypi
 the updater for @uref{https://pypi.python.org, PyPI} packages.
+@item gem
+the updater for @uref{https://rubygems.org, RubyGems} packages.
 @end table
 
 For instance, the following command only checks for updates of Emacs
diff --git a/guix/import/gem.scm b/guix/import/gem.scm
index 4b2a253..b46622f 100644
--- a/guix/import/gem.scm
+++ b/guix/import/gem.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 David Thompson <da...@gnu.org>
+;;; Copryight © 2016 Ben Woodcroft <donttrust...@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,21 +20,33 @@
 (define-module (guix import gem)
   #:use-module (ice-9 match)
   #:use-module (ice-9 pretty-print)
+  #:use-module (srfi srfi-1)
   #:use-module (rnrs bytevectors)
   #:use-module (json)
   #:use-module (web uri)
+  #:use-module ((guix download) #:prefix download:)
   #:use-module (guix import utils)
   #:use-module (guix import json)
   #:use-module (guix packages)
+  #:use-module (guix upstream)
   #:use-module (guix licenses)
   #:use-module (guix base32)
-  #:export (gem->guix-package))
+  #:use-module (guix build-system ruby)
+  #:use-module (gnu packages)
+  #:export (gem->guix-package
+%gem-updater))
 
 (define (rubygems-fetch name)
   "Return an alist representation of the RubyGems metadata for the package 
NAME,
 or #f on failure."
-  (json-fetch
-   (string-append "https://rubygems.org/api/v1/gems/; name ".json")))
+  ;; XXX: We want to silence the download progress report, which is especially
+  ;; annoying for 'guix refresh', but we have to use a file port.
+  (call-with-output-file "/dev/null"
+(lambda (null)
+  (with-error-to-port null
+(lambda ()
+  (json-fetch
+   (string-append "https://rubygems.org/api/v1/gems/; name 
".json")))
 
 (define (ruby-package-name name)
   "Given the NAME of a package on RubyGems, return a Guix-compliant name for
@@ -132,3 +145,47 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and 
LICENSES."
   (assoc-ref package "licenses"
(make-gem-sexp name version hash home-page synopsis
   description dependencies licenses)
+
+(define (guix-package->gem-name package)
+  "Given a PACKAGE built from rubygems.org, return the name of the
+package on RubyGems."
+  (let ((source-url (and=> (package-source package) origin-uri)))
+;; The URL has the form:
+;; 'https://rubygems.org/downloads/' +
+;; package name + '-' + version + '.gem'
+;; e.g. "https://rubygems.org/downloads/hashery-2.1.1.gem;
+(substring source-url 31 (string-rindex source-url #\-
+
+(define (gem-package? package)
+  "Return true if PACKAGE is a gem package from RubyGems."
+
+  (define (rubygems-url? url)
+(string-prefix? "https://rubygems.org/downloads/; url))
+
+  (let ((source-url (and=> (package-source package) origin-uri))
+(fetch-method (and=> (package-source package) origin-method)))
+(and (eq? fetch-method download:url-fetch)
+ (match source-url
+   ((? string?)
+(rubygems-url? source-url))
+   ((source-url ...)
+(any rubygems-url? source-url))
+
+(define (latest-release guix-package)
+  "Return an  for the latest release of GUIX-PACKAGE."
+  (let* ((gem-name (guix-package->gem-name
+(specification->package guix-package)))
+ (metadata (rubygems-fetch gem-name))
+ (version (assoc-ref metadata "version"))
+ (url (rubygems-uri gem-name version)))
+(upstream-source
+ (package guix-package)
+ (version version)
+ (urls (list url)
+
+(define %gem-updater
+  (upstream-updater
+   (n

branch master updated (56f5f92 -> fbc5b81)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  56f5f92   gnu: nix: Update to 1.11.2.
   new  fbc5b81   import: gem: Add updater.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 doc/guix.texi|2 +
 guix/import/gem.scm  |   63 +++--
 guix/scripts/refresh.scm |5 +++-
 3 files changed, 66 insertions(+), 4 deletions(-)

01/01: gnu: prodigal: Update to 2.6.3.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e70f7a230619dbfe99fefd9d097a0f3004cf9b02
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Feb 16 07:17:39 2016 +1000

gnu: prodigal: Update to 2.6.3.

* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.
---
 gnu/packages/bioinformatics.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6d62632..899447d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2358,7 +2358,7 @@ generated using the PacBio Iso-Seq protocol.")
 (define-public prodigal
   (package
 (name "prodigal")
-(version "2.6.2")
+(version "2.6.3")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -2367,7 +2367,7 @@ generated using the PacBio Iso-Seq protocol.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284"
+"17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"
 (build-system gnu-build-system)
 (arguments
  `(#:tests? #f ;no check target

branch master updated (7fe8ad7 -> e70f7a2)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  7fe8ad7   gnu: polkit-qt: Build with qt-5.
   new  e70f7a2   gnu: prodigal: Update to 2.6.3.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

02/02: gnu: vsearch: Update to 1.10.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit cf6edaba741e2e45d87feed514774cb6667a1074
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Mon Feb 15 22:22:01 2016 +1000

gnu: vsearch: Update to 1.10.0.

* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0.
[origin]: Adapt to changes in bundling of cityhash.
---
 gnu/packages/bioinformatics.scm |   27 +++
 1 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 74761c0..47d4893 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,3 +1,4 @@
+
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rek...@elephly.net>
 ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrust...@gmail.com>
@@ -3353,7 +3354,7 @@ data in the form of VCF files.")
 (define-public vsearch
   (package
 (name "vsearch")
-(version "1.4.1")
+(version "1.10.0")
 (source
  (origin
(method url-fetch)
@@ -3363,7 +3364,7 @@ data in the form of VCF files.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "0b1359wbzgb2cm04h7dq05v80vik88hnsv298xxd1q1f2q4ydni7"))
+ "1i3bad7gnn2y3a1yfixzshd99xdkjc8w5bxzgifpysc6jiljwvb5"))
(modules '((guix build utils)))
(snippet
 '(begin
@@ -3373,14 +3374,24 @@ data in the form of VCF files.")
 -O3 -mtune=native -Wall -Wsign-compare")
   (string-append "AM_CXXFLAGS=-lcityhash"
  " -O3 -Wall -Wsign-compare"))
- (("^__top_builddir__bin_vsearch_SOURCES = cityhash/city.h ")
+ (("^__top_builddir__bin_vsearch_SOURCES = city.h ")
   "__top_builddir__bin_vsearch_SOURCES = \\")
- (("^cityhash/config.h ") "\\")
- (("^cityhash/city.cc ") "\\"))
+ (("^city.h ") "\\")
+ (("^citycrc.h ") "\\")
+ (("^libcityhash_a.*") "")
+ (("noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a \
+libcityhash.a")
+  "noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a")
+ (("__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
+libcpu_sse2.a libcityhash.a")
+  "__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
+libcpu_sse2.a -lcityhash"))
(substitute* "src/vsearch.h"
- (("^\\#include \"cityhash/city.h\"")
-  "#include "))
-   (delete-file-recursively "src/cityhash")
+ (("^\\#include \"city.h\"") "#include ")
+ (("^\\#include \"citycrc.h\"") "#include "))
+   (delete-file "src/city.h")
+   (delete-file "src/citycrc.h")
+   (delete-file "src/city.cc")
#t
 (build-system gnu-build-system)
 (arguments

01/02: gnu: cityhash: Install citycrc.h.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a64a8c465dd2c74fa064f7d2b0c20430022d3248
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Mon Feb 15 22:11:13 2016 +1000

gnu: cityhash: Install citycrc.h.

* gnu/packages/textutils.scm (cityhash)[arguments]: Install citycrc.h.
[version]: Use standardised format, increment to 1.1-2.
---
 gnu/packages/textutils.scm |   31 +--
 1 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index f2c60dd..6f3782f 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayi...@gmail.com>
 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rek...@elephly.net>
-;;; Copyright © 2015 Ben Woodcroft <donttrust...@gmail.com>
+;;; Copyright © 2015, 2016 Ben Woodcroft <donttrust...@gmail.com>
 ;;; Copyright © 2015 Roel Janssen <r...@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -152,11 +152,10 @@ the Hannon Lab.")
 (license license:agpl3+)))
 
 (define-public cityhash
-  (let ((commit "8af9b8c")
-(revision "1"))
+  (let ((commit "8af9b8c"))
 (package
   (name "cityhash")
-  (version (string-append "1.1." revision "." commit))
+  (version (string-append "1.1-2." commit))
   (source (origin
 (method git-fetch)
 (uri (git-reference
@@ -166,13 +165,25 @@ the Hannon Lab.")
 (sha256
  (base32
   "0n6skf5dv8yfl1ckax8dqhvsbslkwc9158zf2ims0xqdvzsahbi6"
-(build-system gnu-build-system)
-(home-page "https://github.com/google/cityhash;)
-(synopsis "C++ hash functions for strings")
-(description
- "CityHash provides hash functions for strings.  The functions mix the
+  (build-system gnu-build-system)
+  (arguments
+   '(#:make-flags (list "CXXFLAGS=-g -O3")
+ #:phases
+ (modify-phases %standard-phases
+   ;; citycrc is not installed by default but is used by some
+   ;; programs.
+   (add-after 'install 'install-citycrc
+ (lambda* (#:key outputs #:allow-other-keys)
+   (let* ((out (assoc-ref outputs "out"))
+  (include (string-append out "/include")))
+ (install-file "src/citycrc.h" include))
+   #t)
+  (home-page "https://github.com/google/cityhash;)
+  (synopsis "C++ hash functions for strings")
+  (description
+   "CityHash provides hash functions for strings.  The functions mix the
 input bits thoroughly but are not suitable for cryptography.")
-(license license:expat
+  (license license:expat
 
 (define-public libconfig
   (package

branch master updated (e86409c -> cf6edab)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  e86409c   gnu: graphite2: Update to 1.3.5.  Update home-page and 
source URI.
   new  a64a8c4   gnu: cityhash: Install citycrc.h.
   new  cf6edab   gnu: vsearch: Update to 1.10.0.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |   27 +++
 gnu/packages/textutils.scm  |   31 +--
 2 files changed, 40 insertions(+), 18 deletions(-)

01/01: gnu: Update sortmerna to 2.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit ce294c0445aa7c6472bc02d9f83d1171b8d88e77
Author: Ben J. Woodcroft 
Date:   Tue Feb 2 22:39:05 2016 +1000

gnu: Update sortmerna to 2.1.

* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
---
 gnu/packages/bioinformatics.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 992ab30..e277f89 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3144,7 +3144,7 @@ of these reads to align data quickly through a hash-based 
indexing scheme.")
 (define-public sortmerna
   (package
 (name "sortmerna")
-(version "2.0")
+(version "2.1")
 (source
  (origin
(method url-fetch)
@@ -3154,7 +3154,7 @@ of these reads to align data quickly through a hash-based 
indexing scheme.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"
+ "1mc5cf1c7xh0h7xb11vh7gqgzx0qvrfa606cb8ixlfg3f2av58s4"
 (build-system gnu-build-system)
 (outputs '("out"  ;for binaries
"db")) ;for sequence databases

branch master updated (0889321 -> ce294c0)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  0889321   gnu: ntp: Update to 4.2.8p6.
   new  ce294c0   gnu: Update sortmerna to 2.1.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

07/17: gnu: Add ruby-mime-types-data.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 32d1c06ffa2768c473b20a43489b2db22c38b72f
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 09:01:01 2015 +1000

gnu: Add ruby-mime-types-data.

* gnu/packages/ruby.scm (ruby-mime-types-data): New variable.
---
 gnu/packages/ruby.scm |   24 
 1 files changed, 24 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index d9feb71..faad88f 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3083,6 +3083,30 @@ that TURN is no longer being maintained.")
 (home-page "http://rubygems.org/gems/turn;)
 (license license:expat)))
 
+(define-public ruby-mime-types-data
+  (package
+(name "ruby-mime-types-data")
+(version "3.2015.1120")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "mime-types-data" version))
+   (sha256
+(base32
+ "04fzvy02w8d0rrsg8avncn7h58pvwdxj82aps54srb3sam2dkhic"
+(build-system ruby-build-system)
+(native-inputs
+ `(("ruby-hoe" ,ruby-hoe)))
+(synopsis "Registry for information about MIME media type definitions")
+(description
+ "@code{mime-types-data} provides a registry for information about
+Multipurpose Internet Mail Extensions (MIME) media type definitions.  It can
+be used with the Ruby mime-types library or other software to determine
+defined filename extensions for MIME types, or to use filename extensions to
+look up the likely MIME type definitions.")
+(home-page "https://github.com/mime-types/mime-types-data/;)
+(license license:expat)))
+
 (define-public ruby-ansi
   (package
 (name "ruby-ansi")

14/17: gnu: Add ruby-shoulda.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 6f390716b664c5cbebef2130d605925d272e3c0a
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 09:22:43 2015 +1000

gnu: Add ruby-shoulda.

* gnu/packages/ruby.scm (ruby-shoulda): New variable.
---
 gnu/packages/ruby.scm |   29 +
 1 files changed, 29 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 3e53647..373bf5c 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3268,6 +3268,35 @@ more complex, and error-prone.")
(base32
 "0d3ryqcsk1n9y35bx5wxnqbgw4m8b3c79isazdjnnbg8crdp72d0"))
 
+(define-public ruby-shoulda
+  (package
+(name "ruby-shoulda")
+(version "3.5.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "shoulda" version))
+   (sha256
+(base32
+ "0csmf15a7mcinfq54lfa4arp0f4b2jmwva55m0p94hdf3pxnjymy"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (replace 'check
+   ;; Don't run tests to avoid circular dependence with rails.  Instead
+   ;; just import the library to test.
+   (lambda _ (zero? (system* "ruby" "-Ilib" "-r" "shoulda")))
+(propagated-inputs
+ `(("ruby-shoulda-context" ,ruby-shoulda-context)
+   ("ruby-shoulda-matchers" ,ruby-shoulda-matchers-2)))
+(synopsis "Context framework and matchers for testing")
+(description
+ "@code{shoulda} is a meta-package combining @code{shoulda-context} and
+@code{shoulda-matchers} providing tools for writing tests.")
+(home-page "https://github.com/thoughtbot/shoulda;)
+(license license:expat)))
+
 (define-public ruby-ansi
   (package
 (name "ruby-ansi")

13/17: gnu: Add ruby-shoulda-matchers-2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 3885c58b252093b49966a0198d2e2f1d1c8eba8d
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 09:21:51 2015 +1000

gnu: Add ruby-shoulda-matchers-2.

* gnu/packages/ruby.scm (ruby-shoulda-matchers-2): New variable.
---
 gnu/packages/ruby.scm |   11 +++
 1 files changed, 11 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index d876f57..3e53647 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3257,6 +3257,17 @@ more complex, and error-prone.")
 (home-page "https://github.com/thoughtbot/shoulda-matchers;)
 (license license:expat)))
 
+(define-public ruby-shoulda-matchers-2
+  (package
+(inherit ruby-shoulda-matchers)
+(version "2.8.0")
+(source (origin
+  (method url-fetch)
+  (uri (rubygems-uri "shoulda-matchers" version))
+  (sha256
+   (base32
+"0d3ryqcsk1n9y35bx5wxnqbgw4m8b3c79isazdjnnbg8crdp72d0"))
+
 (define-public ruby-ansi
   (package
 (name "ruby-ansi")

09/17: gnu: Add ruby-mime-types.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit d39b606c8874204e6f12a7af9049c3d1615eda25
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 09:05:55 2015 +1000

gnu: Add ruby-mime-types.

* gnu/packages/ruby.scm (ruby-mime-types): New variable.
---
 gnu/packages/ruby.scm |   29 +
 1 files changed, 29 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index a23d75e..312d33c 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3107,6 +3107,35 @@ look up the likely MIME type definitions.")
 (home-page "https://github.com/mime-types/mime-types-data/;)
 (license license:expat)))
 
+(define-public ruby-mime-types
+  (package
+(name "ruby-mime-types")
+(version "3.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "mime-types" version))
+   (sha256
+(base32
+ "1snjc38a9vqvy8j41xld1i1byq9prbl955pbjw7dxqcfcirqlzra"
+(build-system ruby-build-system)
+(propagated-inputs
+ `(("ruby-mime-types-data" ,ruby-mime-types-data)))
+(native-inputs
+ `(("ruby-hoe" ,ruby-hoe)
+   ("ruby-fivemat" ,ruby-fivemat)
+   ("ruby-minitest-focus" ,ruby-minitest-focus)
+   ("ruby-minitest-rg" ,ruby-minitest-rg)
+   ("ruby-minitest-bonus-assertions" ,ruby-minitest-bonus-assertions)))
+(synopsis "Library and registry for MIME content type definitions")
+(description "The mime-types library provides a library and registry for
+information about Multipurpose Internet Mail Extensions (MIME) content type
+definitions.  It can be used to determine defined filename extensions for MIME
+types, or to use filename extensions to look up the likely MIME type
+definitions.")
+(home-page "https://github.com/mime-types/ruby-mime-types;)
+(license license:expat)))
+
 (define-public ruby-fivemat
   (package
 (name "ruby-fivemat")

17/17: gnu: Add ruby-http-cookie.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit d114ceebaca88edc9716e6de9949ce20c11a342f
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 09:27:51 2015 +1000

gnu: Add ruby-http-cookie.

* gnu/packages/ruby.scm (ruby-http-cookie): New variable.
---
 gnu/packages/ruby.scm |   39 +++
 1 files changed, 39 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index ed1bc69..9707874 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3374,6 +3374,45 @@ Suffix List.")
 (home-page "https://github.com/knu/ruby-domain_name;)
 (license license:bsd-2)))
 
+(define-public ruby-http-cookie
+  (package
+(name "ruby-http-cookie")
+(version "1.0.2")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "http-cookie" version))
+   (sha256
+(base32
+ "0cz2fdkngs3jc5w32a6xcl511hy03a7zdiy988jk1sf3bf5v3hdw"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-before 'check 'add-dependency-to-bundler
+   (lambda _
+ ;; Fix NameError
+ (substitute* "Rakefile"
+   (("HTTP::Cookie::VERSION")
+"Bundler::GemHelper.gemspec.version"))
+ #t)
+(propagated-inputs
+ `(("ruby-domain-name" ,ruby-domain-name)))
+(native-inputs
+ `(("rubysimplecov" ,ruby-simplecov)
+   ("bundler" ,bundler)
+   ("ruby-sqlite3" ,ruby-sqlite3)
+   ("ruby-test-unit" ,ruby-test-unit)))
+(synopsis "Handle HTTP Cookies based on RFC 6265")
+(description
+ "@code{HTTP::Cookie} is a Ruby library to handle HTTP Cookies based on
+RFC 6265.  It has been designed with security, standards compliance and
+compatibility in mind, to behave just the same as today's major web browsers.
+It has built-in support for the legacy @code{cookies.txt} and
+@code{cookies.sqlite} formats of Mozilla Firefox.")
+(home-page "https://github.com/sparklemotion/http-cookie;)
+(license license:expat)))
+
 (define-public ruby-ansi
   (package
 (name "ruby-ansi")

05/17: gnu: Add ruby-minitest-bonus-assertions.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e07ef1d625c01e83d8853ea4ece11af07989d585
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 08:56:18 2015 +1000

gnu: Add ruby-minitest-bonus-assertions.

* gnu/packages/ruby.scm (ruby-minitest-bonus-assertions): New variable.
---
 gnu/packages/ruby.scm |   35 +++
 1 files changed, 35 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 964ec1e..00f1460 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1616,6 +1616,41 @@ MiniTest @code{Object#stub} with a global @code{stub} 
method.")
 (home-page "https://github.com/dockyard/minitest-moar;)
 (license license:expat)))
 
+(define-public ruby-minitest-bonus-assertions
+  (package
+(name "ruby-minitest-bonus-assertions")
+(version "2.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "minitest-bonus-assertions" version))
+   (sha256
+(base32
+ "11nrd32kwy61ndg9csk7l1ifya79ghrrv3vsrxj57k50m7na6jkm"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-before 'check 'clean-dependencies
+   (lambda _
+ ;; Remove unneeded require statement that would entail another
+ ;; dependency.
+ (substitute* "test/minitest_config.rb"
+   (("require 'minitest/bisect'") ""))
+ #t)
+(native-inputs
+ `(("ruby-hoe" ,ruby-hoe)
+   ("ruby-minitest-pretty-diff" ,ruby-minitest-pretty-diff)
+   ("ruby-minitest-focus" ,ruby-minitest-focus)
+   ("ruby-minitest-moar" ,ruby-minitest-moar)))
+(synopsis "Bonus assertions for @code{Minitest}")
+(description
+ "Minitest bonus assertions provides extra MiniTest assertions.  For
+instance, it provides @code{assert_true}, @code{assert_false} and
+@code{assert_set_equal}.")
+(home-page "https://github.com/halostatue/minitest-bonus-assertions;)
+(license license:expat)))
+
 (define-public ruby-daemons
   (package
 (name "ruby-daemons")

02/17: gnu: Add ruby-minitest-focus.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 39dc0eb50204f03e95a7a5636e7c28c8e5e0ae99
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed Dec 30 23:22:05 2015 +1000

gnu: Add ruby-minitest-focus.

* gnu/packages/ruby.scm (ruby-minitest-focus): New variable.
---
 gnu/packages/ruby.scm |   25 +
 1 files changed, 25 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 35215cf..774653b 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1521,6 +1521,31 @@ functionality, making it easier to migrate test suites 
from bacon to minitest.")
 (home-page "https://github.com/seattlerb/minitest-bacon;)
 (license license:expat)))
 
+(define-public ruby-minitest-focus
+  (package
+(name "ruby-minitest-focus")
+(version "1.1.2")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "minitest-focus" version))
+   (sha256
+(base32
+ "1zgjslp6d7dzcn8smj595idymgd5j603p9g2jqkfgi28sqbhz6m0"
+(build-system ruby-build-system)
+(propagated-inputs
+ `(("ruby-minitest" ,ruby-minitest)))
+(native-inputs
+ `(("ruby-hoe" ,ruby-hoe)))
+(synopsis "Allows a few specific tests to be focused on")
+(description
+ "@code{minitest-focus} gives the ability focus on a few tests with ease
+without having to use command-line arguments.  It introduces a @code{focus}
+class method for use in testing classes, specifying that the next defined test
+is to be run.")
+(home-page "https://github.com/seattlerb/minitest-focus;)
+(license license:expat)))
+
 (define-public ruby-daemons
   (package
 (name "ruby-daemons")

branch master updated (f66842d -> d114cee)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  f66842d   gnu: Add aria2.
   new  8092e33   gnu: Add ruby-turn.
   new  39dc0eb   gnu: Add ruby-minitest-focus.
   new  99fc5cd   gnu: Add ruby-minitest-pretty-diff.
   new  685d0d2   gnu: Add ruby-minitest-moar.
   new  e07ef1d   gnu: Add ruby-minitest-bonus-assertions.
   new  e582fa9   gnu: Add ruby-minitest-rg.
   new  32d1c06   gnu: Add ruby-mime-types-data.
   new  eb5e0bd   gnu: Add ruby-fivemat.
   new  d39b606   gnu: Add ruby-mime-types.
   new  4fea500   gnu: Add ruby-sqlite3.
   new  4dfa39c   gnu: Add ruby-shoulda-context.
   new  e4fea00   gnu: Add ruby-shoulda-matchers.
   new  3885c58   gnu: Add ruby-shoulda-matchers-2.
   new  6f39071   gnu: Add ruby-shoulda.
   new  3b44bcd   gnu: Add ruby-unf.
   new  5799aad   gnu: Add ruby-domain-name.
   new  d114cee   gnu: Add ruby-http-cookie.

The 17 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/ruby.scm |  518 +
 1 files changed, 518 insertions(+), 0 deletions(-)

08/17: gnu: Add ruby-fivemat.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit eb5e0bd96e94cb770bf75742a1bb400aa7cf4e60
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 09:03:19 2015 +1000

gnu: Add ruby-fivemat.

* gnu/packages/ruby.scm (ruby-fivemat): New variable.
---
 gnu/packages/ruby.scm |   22 ++
 1 files changed, 22 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index faad88f..a23d75e 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3107,6 +3107,28 @@ look up the likely MIME type definitions.")
 (home-page "https://github.com/mime-types/mime-types-data/;)
 (license license:expat)))
 
+(define-public ruby-fivemat
+  (package
+(name "ruby-fivemat")
+(version "1.3.2")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "fivemat" version))
+   (sha256
+(base32
+ "1gvw6g4yc96l2pcyvigahyfsjxpdjx21iiwzvf965zippchdh6gk"
+(build-system ruby-build-system)
+(arguments
+ `(#:tests? #f)) ; no tests
+(synopsis "Each test file given its own line of dots")
+(description
+ "Fivemat is a MiniTest/RSpec/Cucumber formatter that gives each test file
+its own line of dots during testing.  It aims to provide test output that is
+neither too verbose nor too minimal.")
+(home-page "https://github.com/tpope/fivemat;)
+(license license:expat)))
+
 (define-public ruby-ansi
   (package
 (name "ruby-ansi")

15/17: gnu: Add ruby-unf.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 3b44bcdfcdb161dd1109635c449034a0a0f9e7e9
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 09:23:55 2015 +1000

gnu: Add ruby-unf.

* gnu/packages/ruby.scm (ruby-unf): New variable.
---
 gnu/packages/ruby.scm |   37 +
 1 files changed, 37 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 373bf5c..181c279 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3297,6 +3297,43 @@ more complex, and error-prone.")
 (home-page "https://github.com/thoughtbot/shoulda;)
 (license license:expat)))
 
+(define-public ruby-unf
+  (package
+(name "ruby-unf")
+(version "0.1.4")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "unf" version))
+   (sha256
+(base32
+ "0bh2cf73i2ffh4fcpdn9ir4mhq8zi50ik0zqa1braahzadx536a9"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-before 'check 'add-dependency-to-bundler
+   (lambda _
+ ;; test-unit is required but not provided by the bundler
+ ;; environment.  This is fixed in the upstream repository but fix
+ ;; has not been released.
+ (substitute* "Gemfile"
+   (("^gemspec") "gem 'test-unit'\ngemspec"))
+ #t)
+(propagated-inputs
+ `(("ruby-unf-ext" ,ruby-unf-ext)))
+(native-inputs
+ `(("ruby-shoulda" ,ruby-shoulda)
+   ("bundler" ,bundler)
+   ("ruby-test-unit" ,ruby-test-unit)))
+(synopsis "Unicode Normalization Form support to Ruby and JRuby")
+(description
+ "@code{ruby-unf} is a wrapper library to bring Unicode Normalization Form
+support to both Ruby and JRuby.  It uses @code{unf_ext} on CRuby and
+@code{java.text.Normalizer} on JRuby.")
+(home-page "https://github.com/knu/ruby-unf;)
+(license license:bsd-2)))
+
 (define-public ruby-ansi
   (package
 (name "ruby-ansi")

03/17: gnu: Add ruby-minitest-pretty-diff.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 99fc5cd57710a0d74ade9bbf560fec4b2a259122
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed Dec 30 23:36:03 2015 +1000

gnu: Add ruby-minitest-pretty-diff.

* gnu/packages/ruby.scm (ruby-minitest-pretty-diff): New variable.
---
 gnu/packages/ruby.scm |   35 +++
 1 files changed, 35 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 774653b..7cc4266 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1546,6 +1546,41 @@ is to be run.")
 (home-page "https://github.com/seattlerb/minitest-focus;)
 (license license:expat)))
 
+(define-public ruby-minitest-pretty-diff
+  ;; Use git reference because gem is out of date and does not contain testing
+  ;; script.  There are no releases on GitHub.
+  (let ((commit "11f32e930f574225432f42e5e1ef6e7471efe572"))
+(package
+  (name "ruby-minitest-pretty-diff")
+  (version (string-append "0.1-1." (string-take commit 8)))
+  (source (origin
+(method git-fetch)
+(uri (git-reference
+  (url 
"https://github.com/adammck/minitest-pretty_diff.git;)
+  (commit commit)))
+(file-name (string-append name "-" version "-checkout"))
+(sha256
+ (base32
+  "13y5dhmcckhzd83gj1nfwh41iykbjcm2w7y4pr6j6rpqa5as122r"
+  (build-system ruby-build-system)
+  (arguments
+   `(#:phases
+ (modify-phases %standard-phases
+   (replace 'check
+ (lambda _
+   (zero? (system* "script/test")))
+  (native-inputs
+   `(("bundler" ,bundler)
+ ("ruby-turn" ,ruby-turn)))
+  (synopsis "Pretty-print hashes and arrays in MiniTest")
+  (description
+   "@code{minitest-pretty_diff} monkey-patches
+@code{MiniTest::Assertions#mu_pp} to pretty-print hashes and arrays before
+diffing them.  This makes it easier to spot differences between nested
+structures when tests fail.")
+  (home-page "https://github.com/adammck/minitest-pretty_diff;)
+  (license license:expat
+
 (define-public ruby-daemons
   (package
 (name "ruby-daemons")

06/17: gnu: Add ruby-minitest-rg.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e582fa93a8b2f332da06035c6056c377888958c5
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 08:58:44 2015 +1000

gnu: Add ruby-minitest-rg.

* gnu/packages/ruby.scm (ruby-minitest-rg): New variable.
---
 gnu/packages/ruby.scm |   25 +
 1 files changed, 25 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 00f1460..d9feb71 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1651,6 +1651,31 @@ instance, it provides @code{assert_true}, 
@code{assert_false} and
 (home-page "https://github.com/halostatue/minitest-bonus-assertions;)
 (license license:expat)))
 
+(define-public ruby-minitest-rg
+  (package
+(name "ruby-minitest-rg")
+(version "5.2.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "minitest-rg" version))
+   (sha256
+(base32
+ "0sq509ax1x62rd0w10b0hcydcxyk5bxxr3fwrgxv02r8drq2r354"
+(build-system ruby-build-system)
+(arguments
+ ;; Some tests fail even outside Guix, so disable tests.
+ ;; https://github.com/blowmage/minitest-rg/issues/12
+ ;; https://github.com/blowmage/minitest-rg/pull/13
+ `(#:tests? #f))
+(propagated-inputs
+ `(("ruby-minitest" ,ruby-minitest)))
+(synopsis "Coloured output for Minitest")
+(description
+ "@code{minitest-rg} changes the colour of the output from Minitest.")
+(home-page "http://blowmage.com/minitest-rg;)
+(license license:expat)))
+
 (define-public ruby-daemons
   (package
 (name "ruby-daemons")

12/17: gnu: Add ruby-shoulda-matchers.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e4fea00896244635c9e89770315e365879a99105
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 09:12:59 2015 +1000

gnu: Add ruby-shoulda-matchers.

* gnu/packages/ruby.scm (ruby-shoulda-matchers): New variable.
---
 gnu/packages/ruby.scm |   38 ++
 1 files changed, 38 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 0dc3561..d876f57 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3219,6 +3219,44 @@ names.")
 (home-page "https://github.com/thoughtbot/shoulda-context;)
 (license license:expat)))
 
+(define-public ruby-shoulda-matchers
+  (package
+(name "ruby-shoulda-matchers")
+(version "3.0.1")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "shoulda-matchers" version))
+   (sha256
+(base32
+ "1agabvb8i39mjrp3kb78nvhl41xk1i258hdwdlj0fm8nj9yzn1jb"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-before 'build 'fix-import
+   (lambda _
+ ;; A presumed bug reported upstream at
+ ;; https://github.com/thoughtbot/shoulda-matchers/pull/871
+ (substitute* (string-append  "lib/shoulda/matchers/active_model/"
+  "validate_inclusion_of_matcher.rb")
+   (("^require 'bigdecimal'")
+"require 'bigdecimal'; require 'date'"
+ (replace 'check
+   (lambda _
+ ;; Do not run tests to avoid circular dependence with rails.  
Instead
+ ;; just import the library to test.
+ (zero? (system* "ruby" "-Ilib" "-r" "shoulda-matchers")))
+(propagated-inputs
+ `(("ruby-activesupport" ,ruby-activesupport)))
+(synopsis "Collection of testing matchers extracted from Shoulda")
+(description
+ "Shoulda Matchers provides RSpec- and Minitest-compatible one-liners that
+test common Rails functionality.  These tests would otherwise be much longer,
+more complex, and error-prone.")
+(home-page "https://github.com/thoughtbot/shoulda-matchers;)
+(license license:expat)))
+
 (define-public ruby-ansi
   (package
 (name "ruby-ansi")

04/17: gnu: Add ruby-minitest-moar.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 685d0d2fbeade48b5da6e1bee421ea42ca6cf202
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 07:30:37 2015 +1000

gnu: Add ruby-minitest-moar.

* gnu/packages/ruby.scm (ruby-minitest-moar): New variable.
---
 gnu/packages/ruby.scm |   35 +++
 1 files changed, 35 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 7cc4266..964ec1e 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1581,6 +1581,41 @@ structures when tests fail.")
   (home-page "https://github.com/adammck/minitest-pretty_diff;)
   (license license:expat
 
+(define-public ruby-minitest-moar
+  (package
+(name "ruby-minitest-moar")
+(version "0.0.4")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "minitest-moar" version))
+   (sha256
+(base32
+ "0nb83blrsab92gcy6nfpw39njys7zisia8pw4igzzfzfl51cis0x"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-before 'check 'clean-dependencies
+   (lambda _
+ ;; Remove all gems defined in the Gemfile because these are not
+ ;; truly needed.
+ (substitute* "Gemfile"
+   (("gem .*") ""))
+ ;; Remove byebug as not needed to run tests.
+ (substitute* "test/test_helper.rb"
+   (("require 'byebug'") ""))
+ #t)
+(native-inputs
+ `(("bundler" ,bundler)
+   ("ruby-minitest" ,ruby-minitest)))
+(synopsis "Extra features and changes to MiniTest")
+(description "@code{MiniTest Moar} add some additional features and
+changes some default behaviours in MiniTest.  For instance, Moar replaces the
+MiniTest @code{Object#stub} with a global @code{stub} method.")
+(home-page "https://github.com/dockyard/minitest-moar;)
+(license license:expat)))
+
 (define-public ruby-daemons
   (package
 (name "ruby-daemons")

16/17: gnu: Add ruby-domain-name.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 5799aadde41ea576c158ddf027ea8d16f47c91ac
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Thu Dec 31 09:25:45 2015 +1000

gnu: Add ruby-domain-name.

* gnu/packages/ruby.scm (ruby-domain-name): New variable.
---
 gnu/packages/ruby.scm |   40 
 1 files changed, 40 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 181c279..ed1bc69 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3334,6 +3334,46 @@ support to both Ruby and JRuby.  It uses @code{unf_ext} 
on CRuby and
 (home-page "https://github.com/knu/ruby-unf;)
 (license license:bsd-2)))
 
+(define-public ruby-domain-name
+  (package
+(name "ruby-domain-name")
+(version "0.5.25")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "domain_name" version))
+   (sha256
+(base32
+ "16qvfrmcwlzz073aas55mpw2nhyhjcn96s524w0g1wlml242hjav"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-before 'check 'fix-versions
+   (lambda _
+ ;; Fix NameError that appears to already be fixed upstream.
+ (substitute* "Rakefile"
+   (("DomainName::VERSION")
+"Bundler::GemHelper.gemspec.version"))
+ ;; Loosen unnecessarily strict test-unit version specification.
+ (substitute* "domain_name.gemspec"
+   ((", \\[\\\"~> 2.5.5") ", [\">0"))
+ #t)
+(propagated-inputs
+ `(("ruby-unf" ,ruby-unf)))
+(native-inputs
+ `(("ruby-shoulda" ,ruby-shoulda)
+   ("bundler" ,bundler)
+   ("ruby-test-unit" ,ruby-test-unit)))
+(synopsis "Domain name manipulation library")
+(description
+ "@code{domain_name} is a Domain name manipulation library.  It parses a
+domain name ready for extracting the registered domain and TLD (Top Level
+Domain).  It can also be used for cookie domain validation based on the Public
+Suffix List.")
+(home-page "https://github.com/knu/ruby-domain_name;)
+(license license:bsd-2)))
+
 (define-public ruby-ansi
   (package
 (name "ruby-ansi")

01/17: gnu: Add ruby-turn.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 8092e33376f3cdd69e5e44774be8876f6f1e6f72
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed Dec 30 23:19:10 2015 +1000

gnu: Add ruby-turn.

* gnu/packages/ruby.scm (ruby-turn): New variable.
---
 gnu/packages/ruby.scm |   33 +
 1 files changed, 33 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index af7b1af..35215cf 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2895,6 +2895,39 @@ used to create both network servers and clients.")
 (home-page "http://rubyeventmachine.com;)
 (license (list license:ruby license:gpl3 ; GPLv3 only AFAICT
 
+(define-public ruby-turn
+  (package
+(name "ruby-turn")
+(version "0.9.7")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "turn" version))
+   (sha256
+(base32
+ "1691rc2sq04cw8mxxh340k2j04ll90kwgcy8ddrp6rligmfrf8fw"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ ;; Tests fail because turn changes its environment so can no longer
+ ;; find test/unit.  Instead simply test if the executable runs
+ ;; without issue.
+ (replace 'check
+   (lambda _
+ (zero? (system* "ruby" "-Ilib" "bin/turn" "-h")))
+(propagated-inputs
+ `(("ruby-ansi" ,ruby-ansi)
+   ("ruby-minitest" ,ruby-minitest-4)))
+(synopsis "Alternate set of alternative runners for MiniTest")
+(description
+ "TURN provides a set of alternative runners for MiniTest which are both
+colorful and informative.  TURN displays each test on a separate line with
+failures being displayed immediately instead of at the end of the tests.  Note
+that TURN is no longer being maintained.")
+(home-page "http://rubygems.org/gems/turn;)
+(license license:expat)))
+
 (define-public ruby-ansi
   (package
 (name "ruby-ansi")

04/11: gnu: Add ruby-ae.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 9273ee8f448ae075b4df62b9ad793c1dcf31b7be
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 14:37:45 2015 +1000

gnu: Add ruby-ae.

* gnu/packages/ruby.scm (ruby-ae): New variable.
---
 gnu/packages/ruby.scm |   32 
 1 files changed, 32 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 53da3fa..5cbf125 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3086,3 +3086,35 @@ somewhere between lower-level testing tools like 
@code{Test::Unit} and
 requirement specifications systems like Cucumber.")
 (home-page "http://rubyworks.github.io/qed;)
 (license license:bsd-2)))
+
+(define-public ruby-ae
+  (package
+(name "ruby-ae")
+(version "1.8.2")
+(source
+ (origin
+   (method url-fetch)
+   ;; Fetch from github so tests are included.
+   (uri (string-append
+ "https://github.com/rubyworks/ae/archive/;
+ version ".tar.gz"))
+   (file-name (string-append name "-" version ".tar.gz"))
+   (sha256
+(base32
+ "147jmkx54x7asy2d8m4dyrhhf4hdx4galpnhwzai030y3cdsfrrl"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (replace 'check
+   (lambda _ (zero? (system* "qed")))
+(propagated-inputs
+ `(("ruby-ansi" ,ruby-ansi)))
+(native-inputs
+ `(("ruby-qed" ,ruby-qed)))
+(synopsis "Assertions library")
+(description
+ "Assertive Expressive (AE) is an assertions library specifically designed
+for reuse by other test frameworks.")
+(home-page "http://rubyworks.github.io/ae;)
+(license license:bsd-2)))

01/11: gnu: Add ruby-rubytest.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 7c8131c76b3a7e5bb0f133c554b46960b3430b70
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 14:13:42 2015 +1000

gnu: Add ruby-rubytest.

* gnu/packages/ruby.scm (ruby-rubytest): New variable.
---
 gnu/packages/ruby.scm |   31 +++
 1 files changed, 31 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index f7a20b8..17dfd4a 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2994,3 +2994,34 @@ to the @code{STDOUT} and @code{STDERR} streams are 
reported, giving extra
 detail to ease debugging.")
 (home-page "http://github.com/wwood/bioruby-commandeer;)
 (license license:expat)))
+
+(define-public ruby-rubytest
+  (package
+(name "ruby-rubytest")
+(version "0.8.1")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "rubytest" version))
+   (sha256
+(base32
+ "19jydsdnkl81i9dhdcr4dc34j0ilm68ff2ngnka1hi38xiw4p5qz"
+(build-system ruby-build-system)
+(arguments
+ ;; Disable regular testing to break the cycle rubytest, qed, brass,
+ ;; rubytest, as well as the cycle rubytest, qed, ansi, rubytest.  Instead
+ ;; simply test that the library can be require'd.
+ `(#:phases
+   (modify-phases %standard-phases
+ (replace 'check
+   (lambda _
+ (zero? (system* "ruby" "-Ilib" "-r" "rubytest")))
+(propagated-inputs
+ `(("ruby-ansi" ,ruby-ansi)))
+(synopsis "Universal test harness for Ruby")
+(description
+ "Rubytest is a testing meta-framework for Ruby.  It can handle any
+compliant test framework and can run tests from multiple frameworks in a
+single pass.")
+(home-page "http://rubyworks.github.io/rubytest;)
+(license license:bsd-2)))

05/11: gnu: Add ruby-lemon.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 78bb471f37dbe6d77bb258c5859861da7038f720
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 14:42:53 2015 +1000

gnu: Add ruby-lemon.

* gnu/packages/ruby.scm (ruby-lemon): New variable.
---
 gnu/packages/ruby.scm |   30 ++
 1 files changed, 30 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 5cbf125..c159e53 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3118,3 +3118,33 @@ requirement specifications systems like Cucumber.")
 for reuse by other test frameworks.")
 (home-page "http://rubyworks.github.io/ae;)
 (license license:bsd-2)))
+
+(define-public ruby-lemon
+  (package
+(name "ruby-lemon")
+(version "0.9.1")
+(source
+(origin
+  (method url-fetch)
+  (uri (rubygems-uri "lemon" version))
+  (sha256
+   (base32
+"0gqhpgjavgpvx23rqpfqcv3d5bs8gc7lr9yvj8kxgp7mfbdc2jcm"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (replace 'check (lambda _ (zero? (system* "qed")))
+(propagated-inputs
+ `(("ruby-ae" ,ruby-ae)
+   ("ruby-ansi" ,ruby-ansi)
+   ("ruby-rubytest" ,ruby-rubytest)))
+(native-inputs
+ `(("ruby-qed" ,ruby-qed)))
+(synopsis "Test framework correlating code structure and test unit")
+(description
+ "Lemon is a unit testing framework that enforces highly formal
+case-to-class and unit-to-method test construction.  This enforcement can help
+focus concern on individual units of behavior.")
+(home-page "http://rubyworks.github.io/lemon;)
+(license license:bsd-2)))

11/11: gnu: Add ruby-ttfunk.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit edf8caae6dd8db81d3dfc69470bb8921684e0f9c
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 15:13:13 2015 +1000

gnu: Add ruby-ttfunk.

* gnu/packages/ruby.scm (ruby-ttfunk): New variable.
---
 gnu/packages/ruby.scm |   41 +
 1 files changed, 41 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 45d2343..af7b1af 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3276,3 +3276,44 @@ binary-to-text encoding.  The main modern use of Ascii85 
is in PostScript and
 @dfn{Portable Document Format} (PDF) file formats.")
 (home-page "https://github.com/datawraith/ascii85gem;)
 (license license:expat)))
+
+(define-public ruby-ttfunk
+  (package
+(name "ruby-ttfunk")
+(version "1.4.0")
+(source
+ (origin
+   (method url-fetch)
+   ;; fetch from github as the gem does not contain testing code
+   (uri (string-append
+ "https://github.com/prawnpdf/ttfunk/archive/;
+ version ".tar.gz"))
+   (file-name (string-append name "-" version ".tar.gz"))
+   (sha256
+(base32
+ "1izq84pnm9niyvkzp8k0vl232q9zj41hwmp9na9fzycfh1pbnsl6"
+(build-system ruby-build-system)
+(arguments
+ `(#:test-target "spec"
+   #:phases
+   (modify-phases %standard-phases
+ (add-before 'check 'remove-rubocop
+   (lambda _
+ ;; remove rubocop as a dependency as not needed for testing
+ (substitute* "ttfunk.gemspec"
+   (("spec.add_development_dependency\\('rubocop'.*") ""))
+ (substitute* "Rakefile"
+   (("require 'rubocop/rake_task'") "")
+   (("Rubocop::RakeTask.new") ""))
+ #t)
+(native-inputs
+ `(("ruby-rspec" ,ruby-rspec)
+   ("bundler" ,bundler)))
+(synopsis "Font metrics parser for the Prawn PDF generator")
+(description
+ "TTFunk is a TrueType font parser written in pure Ruby.  It is used as
+part of the Prawn PDF generator.")
+(home-page "https://github.com/prawnpdf/ttfunk;)
+;; From the README: "Matz's terms for Ruby, GPLv2, or GPLv3. See LICENSE
+;; for details."
+(license (list license:gpl2 license:gpl3 license:ruby

branch master updated (a78d62f -> edf8caa)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  a78d62f   gnu: sra-tools: Update to 2.5.7.
   new  7c8131c   gnu: Add ruby-rubytest.
   new  90fcedf   gnu: Add ruby-brass.
   new  120fc74   gnu: Add ruby-qed.
   new  9273ee8   gnu: Add ruby-ae.
   new  78bb471   gnu: Add ruby-lemon.
   new  0832804   gnu: Add ruby-rubytest-cli.
   new  72ccbfe   gnu: Add ruby-hashery.
   new  1f1d71e   gnu: Add ruby-rc4.
   new  f3e085a   gnu: Add ruby-afm.
   new  acb6be4   gnu: Add ruby-ascii85.
   new  edf8caa   gnu: Add ruby-ttfunk.

The 11 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/ruby.scm |  323 +
 1 files changed, 323 insertions(+), 0 deletions(-)

10/11: gnu: Add ruby-ascii85.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit acb6be429850187ecf078579de19557a9ff31eec
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 15:05:18 2015 +1000

gnu: Add ruby-ascii85.

* gnu/packages/ruby.scm (ruby-ascii85): New variable.
---
 gnu/packages/ruby.scm |   22 ++
 1 files changed, 22 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index e1a36aa..45d2343 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3254,3 +3254,25 @@ specific use case.")
 files and use the data therein.")
 (home-page "http://github.com/halfbyte/afm;)
 (license license:expat)))
+
+(define-public ruby-ascii85
+  (package
+(name "ruby-ascii85")
+(version "1.0.2")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "Ascii85" version))
+   (sha256
+(base32
+ "0j95sbxd18kc8rhcnvl1w37kflqpax1r12h1x47gh4xxn3mz4m7q"
+(build-system ruby-build-system)
+(native-inputs
+ `(("bundler" ,bundler)))
+(synopsis "Encode and decode Ascii85 binary-to-text encoding")
+(description
+ "This library provides methods to encode and decode Ascii85
+binary-to-text encoding.  The main modern use of Ascii85 is in PostScript and
+@dfn{Portable Document Format} (PDF) file formats.")
+(home-page "https://github.com/datawraith/ascii85gem;)
+(license license:expat)))

06/11: gnu: Add ruby-rubytest-cli.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 0832804ed582f01c4edc78d87741642da143003b
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 14:45:17 2015 +1000

gnu: Add ruby-rubytest-cli.

* gnu/packages/ruby.scm (ruby-rubytest-cli): New variable.
---
 gnu/packages/ruby.scm |   24 
 1 files changed, 24 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index c159e53..6e34754 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3148,3 +3148,27 @@ case-to-class and unit-to-method test construction.  
This enforcement can help
 focus concern on individual units of behavior.")
 (home-page "http://rubyworks.github.io/lemon;)
 (license license:bsd-2)))
+
+(define-public ruby-rubytest-cli
+  (package
+(name "ruby-rubytest-cli")
+(version "0.2.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "rubytest-cli" version))
+   (sha256
+(base32
+ "0n7hv4k1ba4fm3i98c6ydbsqhkxgbp52mhi70ba1x3mqzfvk438p"
+(build-system ruby-build-system)
+(arguments
+ `(#:tests? #f)) ; no tests
+(propagated-inputs
+ `(("ruby-ansi" ,ruby-ansi)
+   ("ruby-rubytest" ,ruby-rubytest)))
+(synopsis "Command-line interface for rubytest")
+(description
+ "Rubytest CLI is a command-line interface for running tests for
+Rubytest-based test frameworks.  It provides the @code{rubytest} executable.")
+(home-page "http://rubyworks.github.io/rubytest-cli;)
+(license license:bsd-2)))

03/11: gnu: Add ruby-qed.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 120fc74b21861138e859f740fbeb02afe3f43a45
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 14:36:20 2015 +1000

gnu: Add ruby-qed.

* gnu/packages/ruby.scm (ruby-qed): New variable.
---
 gnu/packages/ruby.scm |   33 +
 1 files changed, 33 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index bd03d49..53da3fa 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3053,3 +3053,36 @@ foundational assertions framework for other assertion 
and test frameworks to
 make use of.")
 (home-page "http://rubyworks.github.io/brass;)
 (license license:bsd-2)))
+
+(define-public ruby-qed
+  (package
+(name "ruby-qed")
+(version "2.9.2")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "qed" version))
+   (sha256
+(base32
+ "03h4lmlxpcya8j7s2cnyscqlx8v3xl1xgsw5y1wk1scxcgz2vbmr"
+(build-system ruby-build-system)
+(arguments
+ ;; Disable testing to break the cycle qed, ansi, qed, among others.
+ ;; Instead simply test that the executable runs using --copyright.
+ `(#:phases
+   (modify-phases %standard-phases
+ (replace 'check
+   (lambda _
+ (zero? (system* "ruby" "-Ilib" "bin/qed" "--copyright")))
+(propagated-inputs
+ `(("ruby-ansi" ,ruby-ansi)
+   ("ruby-brass" ,ruby-brass)))
+(synopsis "Test framework utilizing literate programming techniques")
+(description
+ "@dfn{Quality Ensured Demonstrations} (QED) is a test framework for
+@dfn{Test Driven Development} (TDD) and @dfn{Behaviour Driven
+Development} (BDD) utilizing Literate Programming techniques.  QED sits
+somewhere between lower-level testing tools like @code{Test::Unit} and
+requirement specifications systems like Cucumber.")
+(home-page "http://rubyworks.github.io/qed;)
+(license license:bsd-2)))

07/11: gnu: Add ruby-hashery.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 72ccbfe3141a471a3dd403a19a3cdad7ab270f83
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 14:51:34 2015 +1000

gnu: Add ruby-hashery.

* gnu/packages/ruby.scm (ruby-hashery): New variable.
---
 gnu/packages/ruby.scm |   35 +++
 1 files changed, 35 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 6e34754..e107714 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3172,3 +3172,38 @@ focus concern on individual units of behavior.")
 Rubytest-based test frameworks.  It provides the @code{rubytest} executable.")
 (home-page "http://rubyworks.github.io/rubytest-cli;)
 (license license:bsd-2)))
+
+(define-public ruby-hashery
+  (package
+(name "ruby-hashery")
+(version "2.1.1")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "hashery" version))
+   (sha256
+(base32
+ "0xawbljsjarl9l7700bka672ixwznzwih4s9i38p1y9mp8hyx54g"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (replace 'check
+   (lambda _
+ (and (zero? (system* "qed"))
+  (zero? (system* "rubytest" "-Ilib" "-Itest" "test/"
+(native-inputs
+ `(("ruby-rubytest-cli" ,ruby-rubytest-cli)
+   ("ruby-qed" ,ruby-qed)
+   ("ruby-lemon" ,ruby-lemon)))
+(synopsis "Hash-like classes with extra features")
+(description
+ "The Hashery is a tight collection of @code{Hash}-like classes.
+Included are the auto-sorting @code{Dictionary} class, the efficient
+@code{LRUHash}, the flexible @code{OpenHash} and the convenient
+@code{KeyHash}.  Nearly every class is a subclass of the @code{CRUDHash} which
+defines a CRUD (Create, Read, Update and Delete) model on top of Ruby's
+standard @code{Hash} making it possible to subclass and augment to fit any
+specific use case.")
+(home-page "http://rubyworks.github.io/hashery;)
+(license license:bsd-2)))

08/11: gnu: Add ruby-rc4.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 1f1d71e09f1bc66ece977ed2e7be229c38cd0f5f
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 14:52:04 2015 +1000

gnu: Add ruby-rc4.

* gnu/packages/ruby.scm (ruby-rc4): New variable.
---
 gnu/packages/ruby.scm |   26 ++
 1 files changed, 26 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index e107714..fdfd936 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3207,3 +3207,29 @@ standard @code{Hash} making it possible to subclass and 
augment to fit any
 specific use case.")
 (home-page "http://rubyworks.github.io/hashery;)
 (license license:bsd-2)))
+
+(define-public ruby-rc4
+  (package
+(name "ruby-rc4")
+(version "0.1.5")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "ruby-rc4" version))
+   (sha256
+(base32
+ "00vci475258mmbvsdqkmqadlwn6gj9m01sp7b5a3zd90knil1k00"
+(build-system ruby-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (replace 'check
+   (lambda _
+ (zero? (system* "rspec" "spec/rc4_spec.rb")))
+(native-inputs
+ `(("ruby-rspec" ,ruby-rspec-2)))
+(synopsis "Implementation of the RC4 algorithm")
+(description
+ "RubyRC4 is a pure Ruby implementation of the RC4 algorithm.")
+(home-page "https://github.com/caiges/Ruby-RC4;)
+(license license:expat)))

09/11: gnu: Add ruby-afm.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit f3e085a8d57070f7507b6a4624221fbec4c8addf
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 15:00:15 2015 +1000

gnu: Add ruby-afm.

* gnu/packages/ruby.scm (ruby-afm): New variable.
---
 gnu/packages/ruby.scm |   21 +
 1 files changed, 21 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index fdfd936..e1a36aa 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3233,3 +3233,24 @@ specific use case.")
  "RubyRC4 is a pure Ruby implementation of the RC4 algorithm.")
 (home-page "https://github.com/caiges/Ruby-RC4;)
 (license license:expat)))
+
+(define-public ruby-afm
+  (package
+(name "ruby-afm")
+(version "0.2.2")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "afm" version))
+   (sha256
+(base32
+ "06kj9hgd0z8pj27bxp2diwqh6fv7qhwwm17z64rhdc4sfn76jgn8"
+(build-system ruby-build-system)
+(native-inputs
+ `(("bundler" ,bundler)))
+(synopsis "Read Adobe Font Metrics (afm) files")
+(description
+ "This library provides methods to read @dfn{Adobe Font Metrics} (afm)
+files and use the data therein.")
+(home-page "http://github.com/halfbyte/afm;)
+(license license:expat)))

02/11: gnu: Add ruby-brass.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 90fcedf22030655f0c79fec663276a9e5228c217
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Dec 29 14:16:42 2015 +1000

gnu: Add ruby-brass.

* gnu/packages/ruby.scm (ruby-brass): New variable.
---
 gnu/packages/ruby.scm |   28 
 1 files changed, 28 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 17dfd4a..bd03d49 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3025,3 +3025,31 @@ compliant test framework and can run tests from multiple 
frameworks in a
 single pass.")
 (home-page "http://rubyworks.github.io/rubytest;)
 (license license:bsd-2)))
+
+(define-public ruby-brass
+  (package
+(name "ruby-brass")
+(version "1.2.1")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "brass" version))
+   (sha256
+(base32
+ "154lp8rp1vmg60ri1j4cb8hqlw37z7bn575h899v8hzxwi11sxka"
+(build-system ruby-build-system)
+(arguments
+ ;; Disable tests to break the cycle brass, lemon, ae, qed, brass.
+ ;; Instead simply test that the library can be require'd.
+ `(#:phases
+   (modify-phases %standard-phases
+ (replace 'check
+   (lambda _
+ (zero? (system* "ruby" "-Ilib" "-r" "brass")))
+(synopsis "Basic foundational assertions framework")
+(description
+ "BRASS (Bare-Metal Ruby Assertion System Standard) is a basic
+foundational assertions framework for other assertion and test frameworks to
+make use of.")
+(home-page "http://rubyworks.github.io/brass;)
+(license license:bsd-2)))

01/03: gnu: ngs-sdk: Update to 1.2.3.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit d3b39bc231d95548b56e1d22c1238b9babbfd45c
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Jan 26 10:40:26 2016 +1000

gnu: ngs-sdk: Update to 1.2.3.

gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
---
 gnu/packages/bioinformatics.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a9df676..1f53186 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2647,7 +2647,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
 (define-public ngs-sdk
   (package
 (name "ngs-sdk")
-(version "1.2.2")
+(version "1.2.3")
 (source
  (origin
(method url-fetch)
@@ -2657,7 +2657,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "0rvq61zfw2h9jcz6a33b9xrl20r7s5a9rldvv6rs2qy42khpmf5j"
+ "15074fdi94c6pjy83hhk22r86kfvzpaz2i07h3rqg9yy6x3w0pk2"
 (build-system gnu-build-system)
 (arguments
  `(#:parallel-build? #f ; not supported

branch master updated (0833d0c -> a78d62f)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  0833d0c   gnu: aspell-dict-en: Update to 2016.01.19-0.
   new  d3b39bc   gnu: ngs-sdk: Update to 1.2.3.
   new  fe91666   gnu: ncbi-vdb: Update to 2.5.7.
   new  a78d62f   gnu: sra-tools: Update to 2.5.7.

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |   12 ++--
 1 files changed, 6 insertions(+), 6 deletions(-)

03/03: gnu: sra-tools: Update to 2.5.7.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a78d62f4323bac9d93bda73cfb4251c47f6675c9
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Jan 26 10:48:21 2016 +1000

gnu: sra-tools: Update to 2.5.7.

* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
---
 gnu/packages/bioinformatics.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4fb0819..992ab30 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2951,7 +2951,7 @@ complexity samples.")
 (define-public sra-tools
   (package
 (name "sra-tools")
-(version "2.5.4")
+(version "2.5.7")
 (source
  (origin
(method url-fetch)
@@ -2961,7 +2961,7 @@ complexity samples.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1rxxc8a34g70jcaa2j8sys2x93amlbc24k7az39wldhkzgi96825"
+ "0q93qg744x787d08qmjmdafki1wkbvkdwynayjnjd454gkd26jl5"
 (build-system gnu-build-system)
 (arguments
  `(#:parallel-build? #f ; not supported

02/03: gnu: ncbi-vdb: Update to 2.5.7.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit fe91666b79c070417331a6fd3cc0afd5200558f9
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Tue Jan 26 10:45:10 2016 +1000

gnu: ncbi-vdb: Update to 2.5.7.

gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
---
 gnu/packages/bioinformatics.scm |4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f53186..4fb0819 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2711,7 +2711,7 @@ simultaneously.")
 (define-public ncbi-vdb
   (package
 (name "ncbi-vdb")
-(version "2.5.4")
+(version "2.5.7")
 (source
  (origin
(method url-fetch)
@@ -2721,7 +2721,7 @@ simultaneously.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1rcnyc4xkdfcjww2i0s0qrbapys0cxbjcx2sy3qkpslf9f400fgj"
+ "0hay5hy8ynva3mi5wbn4wmq1q23qwxc3aqzbb86hg3x4f1r73270"
 (build-system gnu-build-system)
 (arguments
  `(#:parallel-build? #f ; not supported

branch master updated (880d647 -> 23f3cbb)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  880d647   doc: Add policy about version numbers for VCS snapshots.
   new  23f3cbb   gnu: Add pixz.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/compression.scm |   29 +
 1 files changed, 29 insertions(+), 0 deletions(-)

01/01: gnu: Add pixz.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 23f3cbb8de530e7219c56772334032ab7d90a480
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Mon Jan 25 08:31:14 2016 +1000

gnu: Add pixz.

* gnu/packages/compression.scm (pixz): New variable.
---
 gnu/packages/compression.scm |   29 +
 1 files changed, 29 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index fd3a9ce..0f27fa9 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2015 Leo Famulari <l...@famulari.name>
 ;;; Copyright © 2015 Jeff Mickey <j...@codemac.net>
 ;;; Copyright © 2015 Efraim Flashner <efr...@flashner.co.il>
+;;; Copyright © 2016 Ben Woodcroft <donttrust...@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,8 +33,10 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
+  #:use-module (gnu packages backup)
   #:use-module (gnu packages base)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages valgrind)
   #:use-module ((srfi srfi-1) #:select (last)))
 
@@ -659,3 +662,29 @@ multiple processors and multiple cores when compressing 
data.")
 ;; Things under zopfli/ are under ASL2.0, but 4 files at the top-level,
 ;; written by Mark Adler, are under another non-copyleft license.
 (license license:asl2.0)))
+
+(define-public pixz
+  (package
+(name "pixz")
+(version "1.0.6")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"https://github.com/vasi/pixz/releases/download/v; version
+"/pixz-" version ".tar.xz"))
+  (sha256
+   (base32
+"1s3j7zw6j5zi3fhdxg287ndr3wf6swac7z21mqd1pyiln530gi82"
+(build-system gnu-build-system)
+(native-inputs
+ `(("pkg-config" ,pkg-config)
+   ("libarchive" ,libarchive)))
+(home-page "https://github.com/vasi/pixz;)
+(synopsis "Parallel indexing implementation of LZMA")
+(description
+ "The existing XZ Utils provide great compression in the .xz file format,
+but they produce just one big block of compressed data.  Pixz instead produces
+a collection of smaller blocks which makes random access to the original data
+possible and can compress in parallel.  This is especially useful for large
+tarballs.")
+(license license:bsd-2)))

branch master updated (74273b6 -> bcadaf0)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  74273b6   doc: Fix typo in section on offloading.
   new  bcadaf0   gnu: Add sortmerna.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |   43 +++
 1 files changed, 43 insertions(+), 0 deletions(-)

01/01: gnu: Add sortmerna.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit bcadaf00504ef467319475756a1c0516f600bf11
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat Jan 16 13:33:08 2016 +1000

gnu: Add sortmerna.

* gnu/packages/bioinformatics.scm (sortmerna): New variable.
---
 gnu/packages/bioinformatics.scm |   43 +++
 1 files changed, 43 insertions(+), 0 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c8eb2b8..a9df676 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3141,6 +3141,49 @@ optimized for modern read lengths of 100 bases or 
higher, and takes advantage
 of these reads to align data quickly through a hash-based indexing scheme.")
 (license license:asl2.0)))
 
+(define-public sortmerna
+  (package
+(name "sortmerna")
+(version "2.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append
+ "https://github.com/biocore/sortmerna/archive/;
+ version ".tar.gz"))
+   (file-name (string-append name "-" version ".tar.gz"))
+   (sha256
+(base32
+ "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"
+(build-system gnu-build-system)
+(outputs '("out"  ;for binaries
+   "db")) ;for sequence databases
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (replace 'install
+   (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out   (assoc-ref outputs "out"))
+(bin   (string-append out "/bin"))
+(db(assoc-ref outputs "db"))
+(share
+ (string-append db "/share/sortmerna/rRNA_databases")))
+   (install-file "sortmerna" bin)
+   (install-file "indexdb_rna" bin)
+   (for-each (lambda (file)
+   (install-file file share))
+ (find-files "rRNA_databases" ".*fasta"))
+   #t))
+(home-page "http://bioinfo.lifl.fr/RNA/sortmerna;)
+(synopsis "Biological sequence analysis tool for NGS reads")
+(description
+ "SortMeRNA is a biological sequence analysis tool for filtering, mapping
+and operational taxonomic unit (OTU) picking of next generation
+sequencing (NGS) reads.  The core algorithm is based on approximate seeds and
+allows for fast and sensitive analyses of nucleotide sequences.  The main
+application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
+(license license:lgpl3)))
+
 (define-public star
   (package
 (name "star")

01/02: import: gem: Beautify only the description, not the synopsis.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e88d5fa9ebab07d0b23cb3fc0f3f38bd41047e94
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sun Jan 17 09:12:14 2016 +1000

import: gem: Beautify only the description, not the synopsis.

* guix/import/gem.scm (make-gem-sexp): Add synopsis argument.
(gem->guix-package): Pass unbeautified synopsis to make-gem-sexp.
* tests/gem.scm: Adapt it.
---
 guix/import/gem.scm |7 ---
 tests/gem.scm   |2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/guix/import/gem.scm b/guix/import/gem.scm
index 3c42052..4b2a253 100644
--- a/guix/import/gem.scm
+++ b/guix/import/gem.scm
@@ -77,7 +77,7 @@ the package."
 (bytevector-u8-set! bv i (read-byte i))
 (loop (1+ i)))
 
-(define (make-gem-sexp name version hash home-page description
+(define (make-gem-sexp name version hash home-page synopsis description
dependencies licenses)
   "Return the `package' s-expression for a Ruby package with the given NAME,
 VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
@@ -101,7 +101,7 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and 
LICENSES."
  (,'unquote
   ,(string->symbol name
  dependencies)
- (synopsis ,description); nothing better to use
+ (synopsis ,synopsis)
  (description ,description)
  (home-page ,home-page)
  (license ,(match licenses
@@ -117,6 +117,7 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and 
LICENSES."
  (let ((name (assoc-ref package "name"))
(version  (assoc-ref package "version"))
(hash (assoc-ref package "sha"))
+   (synopsis (assoc-ref package "info")) ; nothing better to 
use
(description  (beautify-description
   (assoc-ref package "info")))
(home-page(assoc-ref package "homepage_uri"))
@@ -129,5 +130,5 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and 
LICENSES."
   "runtime")))
(licenses (map string->license
   (assoc-ref package "licenses"
-   (make-gem-sexp name version hash home-page
+   (make-gem-sexp name version hash home-page synopsis
   description dependencies licenses)
diff --git a/tests/gem.scm b/tests/gem.scm
index 9efbda3..ebce809 100644
--- a/tests/gem.scm
+++ b/tests/gem.scm
@@ -69,7 +69,7 @@
(("bundler" ('unquote 'bundler))
 ("ruby-bar" ('unquote 'ruby-bar)
  ('synopsis "A cool gem")
- ('description "A cool gem")
+ ('description "This package provides a cool gem")
  ('home-page "https://example.com;)
  ('license ('list 'expat 'asl2.0)))
#t)

branch master updated (d0bd632 -> a132f7d)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  d0bd632   import: Add Bioconductor importer and updater.
   new  e88d5fa   import: gem: Beautify only the description, not the 
synopsis.
   new  a132f7d   tests: Move beatify-description tests to import-tests.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 Makefile.am  |3 +-
 guix/import/gem.scm  |7 +++--
 tests/cran.scm   |   10 
 tests/gem.scm|2 +-
 tests/{sets.scm => import-utils.scm} |   41 +++--
 5 files changed, 21 insertions(+), 42 deletions(-)
 copy tests/{sets.scm => import-utils.scm} (53%)

02/02: tests: Move beatify-description tests to import-tests.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a132f7d68f4c61133c0c97d8e5125c48f7205ac9
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sun Jan 17 10:20:59 2016 +1000

tests: Move beatify-description tests to import-tests.

Fixes <http://bugs.gnu.org/22391>.

* tests/cran.scm (beautify-description: use double spacing,
beautify-description: transform fragment into sentence). Move
from here ...
* tests/import-utils.scm: ... to here. New file.
* Makefile.am (SCM_TESTS): Add import-utils.
---
 Makefile.am|3 ++-
 tests/cran.scm |   10 --
 tests/import-utils.scm |   39 +++
 3 files changed, 41 insertions(+), 11 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 74bc8b5..7e41990 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -241,7 +241,8 @@ SCM_TESTS = \
   tests/cve.scm\
   tests/file-systems.scm   \
   tests/services.scm   \
-  tests/containers.scm
+  tests/containers.scm \
+  tests/import-utils.scm
 
 if HAVE_GUILE_JSON
 
diff --git a/tests/cran.scm b/tests/cran.scm
index e4f2235..83d2e7f 100644
--- a/tests/cran.scm
+++ b/tests/cran.scm
@@ -86,16 +86,6 @@ Date/Publication: 2015-07-14 14:15:16
   '()
   ((@@ (guix import cran) listify) simple-alist "BadList"))
 
-(test-equal "beautify-description: use double spacing"
-  "This is a package.  It is great.  Trust me Mr.  Hendrix."
-  ((@@ (guix import cran) beautify-description)
-   "This is a package. It is great. Trust me Mr. Hendrix."))
-
-(test-equal "beautify-description: transform fragment into sentence"
-  "This package provides a function to establish world peace"
-  ((@@ (guix import cran) beautify-description)
-   "A function to establish world peace"))
-
 (test-assert "description->package"
   ;; Replace network resources with sample data.
   (mock ((guix build download) url-fetch
diff --git a/tests/import-utils.scm b/tests/import-utils.scm
new file mode 100644
index 000..0836581
--- /dev/null
+++ b/tests/import-utils.scm
@@ -0,0 +1,39 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 Ricardo Wurmus <rek...@elephly.net>
+;;; Copyright © 2016 Ben Woodcroft <donttrust...@gmail.com>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (test-import-utils)
+  #:use-module (guix tests)
+  #:use-module (guix import utils)
+  #:use-module (srfi srfi-64))
+
+(test-begin "import-utils")
+
+(test-equal "beautify-description: use double spacing"
+  "This is a package.  It is great.  Trust me Mr.  Hendrix."
+  (beautify-description
+   "This is a package. It is great. Trust me Mr. Hendrix."))
+
+(test-equal "beautify-description: transform fragment into sentence"
+  "This package provides a function to establish world peace"
+  (beautify-description "A function to establish world peace"))
+
+(test-end "import-utils")
+
+
+(exit (= (test-runner-fail-count (test-runner-current)) 0))

01/02: import: cran: Move beautify-description to utils module.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 2028a2c9607b407d3686ca5791c604ddec45f8f8
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed Jan 6 00:09:19 2016 +1000

import: cran: Move beautify-description to utils module.

* guix/import/cran.scm (beautify-description): Move from here...
* guix/import/utils.scm: ... to here.
---
 guix/import/cran.scm  |   11 ---
 guix/import/utils.scm |   14 +-
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index fc27090..1c30da8 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -136,17 +136,6 @@ empty list when the FIELD cannot be found."
 (string-any char-set:whitespace item)))
   (map string-trim-both items))
 
-(define (beautify-description description)
-  "Improve the package DESCRIPTION by turning a beginning sentence fragment
-into a proper sentence and by using two spaces between sentences."
-  (let ((cleaned (if (string-prefix? "A " description)
- (string-append "This package provides a"
-(substring description 1))
- description)))
-;; Use double spacing between sentences
-(regexp-substitute/global #f "\\. \\b"
-  cleaned 'pre ".  " 'post)))
-
 (define (description->package meta)
   "Return the `package' s-expression for a CRAN package from the alist META,
 which was derived from the R package's DESCRIPTION file."
diff --git a/guix/import/utils.scm b/guix/import/utils.scm
index 0734fa1..44e004b 100644
--- a/guix/import/utils.scm
+++ b/guix/import/utils.scm
@@ -37,7 +37,8 @@
 string->license
 license->symbol
 
-snake-case))
+snake-case
+beautify-description))
 
 (define (factorize-uri uri version)
   "Factorize URI, a package tarball URI as a string, such that any occurrences
@@ -136,3 +137,14 @@ to in the (guix licenses) module, or #f if there is no 
such known license."
   "Return a downcased version of the string STR where underscores are replaced
 with dashes."
   (string-join (string-split (string-downcase str) #\_) "-"))
+
+(define (beautify-description description)
+  "Improve the package DESCRIPTION by turning a beginning sentence fragment
+into a proper sentence and by using two spaces between sentences."
+  (let ((cleaned (if (string-prefix? "A " description)
+ (string-append "This package provides a"
+(substring description 1))
+ description)))
+;; Use double spacing between sentences
+(regexp-substitute/global #f "\\. \\b"
+  cleaned 'pre ".  " 'post)))

branch master updated (6b3a1ce -> 869cda5)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  6b3a1ce   emacs: Fix heading face in "Package Info".
   new  2028a2c   import: cran: Move beautify-description to utils module.
   new  869cda5   import: gem: Beautify description field.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 guix/import/cran.scm  |   11 ---
 guix/import/gem.scm   |3 ++-
 guix/import/utils.scm |   14 +-
 3 files changed, 15 insertions(+), 13 deletions(-)

02/02: import: gem: Beautify description field.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 869cda545d67ff342924780c045ff1c4efa2fd06
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Wed Jan 6 00:17:36 2016 +1000

import: gem: Beautify description field.

* guix/import/gem.scm (gem->guix-package): Use 'beautify-description'.
---
 guix/import/gem.scm |3 ++-
 1 files changed, 2 insertions(+), 1 deletions(-)

diff --git a/guix/import/gem.scm b/guix/import/gem.scm
index c64c4e9..3c42052 100644
--- a/guix/import/gem.scm
+++ b/guix/import/gem.scm
@@ -117,7 +117,8 @@ VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and 
LICENSES."
  (let ((name (assoc-ref package "name"))
(version  (assoc-ref package "version"))
(hash (assoc-ref package "sha"))
-   (description  (assoc-ref package "info"))
+   (description  (beautify-description
+  (assoc-ref package "info")))
(home-page(assoc-ref package "homepage_uri"))
(dependencies (map (lambda (dep)
 (let ((name (assoc-ref dep "name")))

03/03: gnu: orfm: Update to 0.5.3.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 6b6f7d6a0e809c09a0cae47bfe41f2d35f6cf75b
Author: Ben Woodcroft <donttrust...@gmail.com>
Date:   Sat Nov 21 10:37:34 2015 +1000

gnu: orfm: Update to 0.5.3.

* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
---
 gnu/packages/bioinformatics.scm |   10 +++---
 1 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c6531d6..a0b7864 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2079,7 +2079,7 @@ that a read originated from a particular isoform.")
 (define-public orfm
   (package
 (name "orfm")
-(version "0.4.1")
+(version "0.5.3")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -2087,12 +2087,16 @@ that a read originated from a particular isoform.")
 version "/orfm-" version ".tar.gz"))
   (sha256
(base32
-"05fmw145snk646ly076zby0fjav0k7ysbclck5d4s9pmgcfpijc2"
+"0vb6d771gl4mix8bwx919x5ayy9pkj44n7ki336nz3rz2rx4c7gk"
 (build-system gnu-build-system)
 (inputs `(("zlib" ,zlib)))
+(native-inputs
+ `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
+   ("ruby-rspec" ,ruby-rspec)
+   ("ruby" ,ruby)))
 (synopsis "Simple and not slow open reading frame (ORF) caller")
 (description
- "An ORF caller finds stretches of DNA that when translated are not
+ "An ORF caller finds stretches of DNA that, when translated, are not
 interrupted by stop codons.  OrfM finds and prints these ORFs.")
 (home-page "https://github.com/wwood/OrfM;)
 (license license:lgpl3+)))