From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCHES] Update orfm and package test requirements. Date: Wed, 13 Jan 2016 22:48:46 +1000 Message-ID: <569647AE.8050401@uq.edu.au> References: <564FBEA5.6020604@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------070600030305040201050108" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:49415) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aJKrE-0003JD-MB for guix-devel@gnu.org; Wed, 13 Jan 2016 07:49:02 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aJKrB-00077h-Dp for guix-devel@gnu.org; Wed, 13 Jan 2016 07:49:00 -0500 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:53992 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aJKrA-00077O-QO for guix-devel@gnu.org; Wed, 13 Jan 2016 07:48:57 -0500 In-Reply-To: List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ricardo Wurmus Cc: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------070600030305040201050108 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by newmailhub.uq.edu.au id u0DCmmwC016756 Hi, I've been a little while responding as I intending on releasing a new=20 OrfM version before bothering you again. I'd push all this myself but=20 wanted to check one last thing so I don't sound too enthusiastic about=20 my own software. >> + >> +(define-public ruby-bio-commandeer >> + (package >> + (name "ruby-bio-commandeer") >> + (version "0.1.2") >> + (source >> + (origin >> + (method url-fetch) >> + (uri (rubygems-uri "bio-commandeer" version)) >> + (sha256 >> + (base32 >> + "061jxa6km92qfwzl058r2gp8gfcsbyr7m643nw1pxvmjdswaf6ly")))) >> + (build-system ruby-build-system) >> + (arguments >> + `(#:phases >> + (modify-phases %standard-phases >> + (replace 'check >> + ;; Run test without calling 'rake' so that jeweler is >> + ;; not required as an input. >> + (lambda _ >> + (zero? (system* "rspec" "spec/bio-commandeer_spec.rb")))= )))) >> + (propagated-inputs >> + `(("ruby-bio-logger" ,ruby-bio-logger) >> + ("ruby-systemu" ,ruby-systemu))) >> + (native-inputs >> + `(("bundler" ,bundler) >> + ("ruby-rspec" ,ruby-rspec))) >> + (synopsis "Simplified running of shell commands from within Ruby"= ) >> + (description >> + "Bio-commandeer is a dead simple opinionated method of running s= hell >> +commands from within Ruby. The advantage of bio-commandeer over othe= r methods >> +of running external commands is that when something goes wrong, the e= rror >> +message that is reported gives extra detail to ease debugging.") > I don=E2=80=99t really like the first sentence. How about > > =E2=80=9CBio-comandeer lets you run shell commands from within Ruby= . ...=E2=80=9D That wasn't the best sentence before, fo so. I wonder if the replacement=20 is a little bland though. How about (as attached), + "Bio-commandeer provides an opinionated method of running shell=20 commands +from within Ruby. The advantage of bio-commandeer over other methods of +running external commands is that when something goes wrong, the=20 @code{STDOUT} +and @code{STDERR} are reported, giving extra detail to ease debugging.") OK? I made scattered other changes too on top of accepting your=20 suggestions, but I don't imagine a full re-review is necessary. Thanks for the review. ben --------------070600030305040201050108 Content-Type: text/x-patch; name="0003-gnu-orfm-Update-to-0.5.3.patch" Content-Disposition: attachment; filename="0003-gnu-orfm-Update-to-0.5.3.patch" Content-Transfer-Encoding: 7bit >From 5d535f5c465c947140a2917fb9c0aaa31b651102 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 21 Nov 2015 10:37:34 +1000 Subject: [PATCH 3/3] 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 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 82506c1..9c2223f 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+))) -- 2.6.3 --------------070600030305040201050108 Content-Type: text/x-patch; name="0002-gnu-Add-ruby-bio-commandeer.patch" Content-Disposition: attachment; filename="0002-gnu-Add-ruby-bio-commandeer.patch" Content-Transfer-Encoding: 7bit >From 4ded5e53c22ada399c976989dbe10cbf376c4e98 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 21 Nov 2015 10:03:41 +1000 Subject: [PATCH 2/3] gnu: Add ruby-bio-commandeer. * gnu/packages/ruby.scm (ruby-bio-commandeer): New variable. --- gnu/packages/ruby.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 21f282a..59fe1cd 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -2958,3 +2958,38 @@ there is no danger of full pipes or threading issues hanging your process or subprocess.") (home-page "https://github.com/ahoward/systemu") (license license:ruby))) + +(define-public ruby-bio-commandeer + (package + (name "ruby-bio-commandeer") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bio-commandeer" version)) + (sha256 + (base32 + "061jxa6km92qfwzl058r2gp8gfcsbyr7m643nw1pxvmjdswaf6ly")))) + (build-system ruby-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + ;; Run test without calling 'rake' so that jeweler is + ;; not required as an input. + (lambda _ + (zero? (system* "rspec" "spec/bio-commandeer_spec.rb"))))))) + (propagated-inputs + `(("ruby-bio-logger" ,ruby-bio-logger) + ("ruby-systemu" ,ruby-systemu))) + (native-inputs + `(("bundler" ,bundler) + ("ruby-rspec" ,ruby-rspec))) + (synopsis "Simplified running of shell commands from within Ruby") + (description + "Bio-commandeer provides an opinionated method of running shell commands +from within Ruby. The advantage of bio-commandeer over other methods of +running external commands is that when something goes wrong, the @code{STDOUT} +and @code{STDERR} are reported, giving extra detail to ease debugging.") + (home-page "http://github.com/wwood/bioruby-commandeer") + (license license:expat))) -- 2.6.3 --------------070600030305040201050108 Content-Type: text/x-patch; name="0001-gnu-Add-ruby-systemu.patch" Content-Disposition: attachment; filename="0001-gnu-Add-ruby-systemu.patch" Content-Transfer-Encoding: 7bit >From b7d92cbfd47fa9f4807ea72d570d703b78fb59f7 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 21 Nov 2015 10:02:11 +1000 Subject: [PATCH 1/3] gnu: Add ruby-systemu. * gnu/packages/ruby.scm (ruby-systemu): New variable. --- gnu/packages/ruby.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 577be18..21f282a 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -2930,3 +2930,31 @@ methods, a @code{Mixin} module for including color methods, a @code{Logger}, a device.") (home-page "http://rubyworks.github.io/ansi") (license license:bsd-2))) + +(define-public ruby-systemu + (package + (name "ruby-systemu") + (version "2.6.5") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "systemu" version)) + (sha256 + (base32 + "0gmkbakhfci5wnmbfx5i54f25j9zsvbw858yg3jjhfs5n4ad1xq1")))) + (build-system ruby-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'patch-and-set-version + (lambda _ + (setenv "VERSION" ,version) + #t))))) + (synopsis "Capture of stdout/stderr and handling of child processes") + (description + "Systemu can be used on any platform to return status, stdout, and stderr +of any command. Unlike other methods like @code{open3} and @code{popen4} +there is no danger of full pipes or threading issues hanging your process or +subprocess.") + (home-page "https://github.com/ahoward/systemu") + (license license:ruby))) -- 2.6.3 --------------070600030305040201050108--