From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCHES] Update orfm and package test requirements. Date: Fri, 27 Nov 2015 14:19:26 +0100 Message-ID: References: <564FBEA5.6020604@uq.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37988) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a2Iw6-0005k7-FT for guix-devel@gnu.org; Fri, 27 Nov 2015 08:19:42 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a2Iw2-0000YL-H5 for guix-devel@gnu.org; Fri, 27 Nov 2015 08:19:38 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:60364) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a2Iw2-0000Y6-4K for guix-devel@gnu.org; Fri, 27 Nov 2015 08:19:34 -0500 In-Reply-To: <564FBEA5.6020604@uq.edu.au> 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: Ben Woodcroft Cc: "guix-devel@gnu.org" Hi Ben, > + > +(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-version > + (lambda _ > + (substitute* "Rakefile" > + ((" This.lib =3D lib") > + " This.lib =3D 'systemu'") > + ((" version =3D ENV\\['VERSION'\\]") > + (string-append "version=3D'" ,version "'")))))))) Why is this phase needed? Would it be enough to just (setenv "VERSION" ,version) > + (synopsis "Capture of stdout/stderr and handling of child processe= s") > + (description > + "Systemu can be used on any platform to return status, stdout, an= d stderr > +of any command. Unlike other methods like open3/popen4 there is no da= nger of > +full pipes or threading issues hanging your process or subprocess.") Maybe =E2=80=9C@code{open3} or @code{popen4}=E2=80=9D instead of =E2=80=9C= open3/popen4=E2=80=9D. > + (home-page "https://github.com/ahoward/systemu") > + (license license:ruby))) Other than that it looks good to me. > + > +(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 sh= ell > +commands from within Ruby. The advantage of bio-commandeer over other= methods > +of running external commands is that when something goes wrong, the er= ror > +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 > + (home-page > + "http://github.com/wwood/bioruby-commandeer") Could you please put this on one line? > + (license license:expat))) Good! > From 1fe31024e6c78ab7bbdfe7be2c2ac8f4ec1db447 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 0.4.4. > * gnu/packages/bioinformatics.scm (orfm): Update to 0.4.4. > [arguments]: Run intended tests. > [inputs]: Add inputs required for tests. Actually, the message should say =E2=80=9C[native-inputs]=E2=80=9D instea= d of =E2=80=9C[inputs]=E2=80=9D. Other than that it looks good to me. Thanks! ~~ Ricardo