* [PATCHES] Update orfm and package test requirements. @ 2015-11-21 0:45 Ben Woodcroft 2015-11-27 13:19 ` Ricardo Wurmus 0 siblings, 1 reply; 5+ messages in thread From: Ben Woodcroft @ 2015-11-21 0:45 UTC (permalink / raw) To: guix-devel@gnu.org [-- Attachment #1: Type: text/plain, Size: 164 bytes --] Perhaps this set could be seen as a little self-serving given I'm the author, though at least ruby-systemu is more widely used. Thanks in advance for review. ben [-- Attachment #2: 0001-gnu-Add-ruby-systemu.patch --] [-- Type: text/x-patch, Size: 1892 bytes --] From 6aad034b3d40bffe2bec35ed3f7df7ce1537217d Mon Sep 17 00:00:00 2001 From: Ben Woodcroft <donttrustben@gmail.com> 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 | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 7c12421..ad20b73 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -2060,3 +2060,33 @@ programs to concentrate on the implementation of network protocols. It can be 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-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 = lib") + " This.lib = 'systemu'") + ((" version = ENV\\['VERSION'\\]") + (string-append "version='" ,version "'")))))))) + (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 open3/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))) -- 2.1.4 [-- Attachment #3: 0002-gnu-Add-ruby-bio-commandeer.patch --] [-- Type: text/x-patch, Size: 2121 bytes --] From b1981255c06271c8cd4f3fd5291414034714cd2f Mon Sep 17 00:00:00 2001 From: Ben Woodcroft <donttrustben@gmail.com> 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 | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index ad20b73..c964fe3 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -2090,3 +2090,39 @@ of any command. Unlike other methods like open3/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))) + +(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 shell +commands from within Ruby. The advantage of bio-commandeer over other methods +of running external commands is that when something goes wrong, the error +message that is reported gives extra detail to ease debugging.") + (home-page + "http://github.com/wwood/bioruby-commandeer") + (license license:expat))) -- 2.1.4 [-- Attachment #4: 0003-gnu-orfm-Update-to-0.4.4.patch --] [-- Type: text/x-patch, Size: 1640 bytes --] From 1fe31024e6c78ab7bbdfe7be2c2ac8f4ec1db447 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft <donttrustben@gmail.com> 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. --- gnu/packages/bioinformatics.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35cec1e..24a1992 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1878,7 +1878,7 @@ that a read originated from a particular isoform.") (define-public orfm (package (name "orfm") - (version "0.4.1") + (version "0.4.4") (source (origin (method url-fetch) (uri (string-append @@ -1886,9 +1886,15 @@ that a read originated from a particular isoform.") version "/orfm-" version ".tar.gz")) (sha256 (base32 - "05fmw145snk646ly076zby0fjav0k7ysbclck5d4s9pmgcfpijc2")))) + "1pwpy6qwkjjd4jyfln5c4c0009blgar0g7c5wkldbs9mzqrv77di")))) (build-system gnu-build-system) + (arguments + `(#:test-target "test")) (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 -- 2.1.4 ^ permalink raw reply related [flat|nested] 5+ messages in thread
* Re: [PATCHES] Update orfm and package test requirements. 2015-11-21 0:45 [PATCHES] Update orfm and package test requirements Ben Woodcroft @ 2015-11-27 13:19 ` Ricardo Wurmus 2016-01-13 12:48 ` Ben Woodcroft 0 siblings, 1 reply; 5+ messages in thread From: Ricardo Wurmus @ 2015-11-27 13:19 UTC (permalink / raw) 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 = lib") > + " This.lib = 'systemu'") > + ((" version = ENV\\['VERSION'\\]") > + (string-append "version='" ,version "'")))))))) Why is this phase needed? Would it be enough to just (setenv "VERSION" ,version) > + (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 open3/popen4 there is no danger of > +full pipes or threading issues hanging your process or subprocess.") Maybe “@code{open3} or @code{popen4}” instead of “open3/popen4”. > + (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 shell > +commands from within Ruby. The advantage of bio-commandeer over other methods > +of running external commands is that when something goes wrong, the error > +message that is reported gives extra detail to ease debugging.") I don’t really like the first sentence. How about “Bio-comandeer lets you run shell commands from within Ruby. ...” > + (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 <donttrustben@gmail.com> > 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 “[native-inputs]” instead of “[inputs]”. Other than that it looks good to me. Thanks! ~~ Ricardo ^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCHES] Update orfm and package test requirements. 2015-11-27 13:19 ` Ricardo Wurmus @ 2016-01-13 12:48 ` Ben Woodcroft 2016-01-13 13:50 ` Ricardo Wurmus 0 siblings, 1 reply; 5+ messages in thread From: Ben Woodcroft @ 2016-01-13 12:48 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: guix-devel@gnu.org [-- Attachment #1: Type: text/plain, Size: 2359 bytes --] Hi, I've been a little while responding as I intending on releasing a new OrfM version before bothering you again. I'd push all this myself but wanted to check one last thing so I don't sound too enthusiastic about 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 shell >> +commands from within Ruby. The advantage of bio-commandeer over other methods >> +of running external commands is that when something goes wrong, the error >> +message that is reported gives extra detail to ease debugging.") > I don’t really like the first sentence. How about > > “Bio-comandeer lets you run shell commands from within Ruby. ...” That wasn't the best sentence before, fo so. I wonder if the replacement is a little bland though. How about (as attached), + "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.") OK? I made scattered other changes too on top of accepting your suggestions, but I don't imagine a full re-review is necessary. Thanks for the review. ben [-- Attachment #2: 0003-gnu-orfm-Update-to-0.5.3.patch --] [-- Type: text/x-patch, Size: 1817 bytes --] From 5d535f5c465c947140a2917fb9c0aaa31b651102 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft <donttrustben@gmail.com> 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 [-- Attachment #3: 0002-gnu-Add-ruby-bio-commandeer.patch --] [-- Type: text/x-patch, Size: 2069 bytes --] From 4ded5e53c22ada399c976989dbe10cbf376c4e98 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft <donttrustben@gmail.com> 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 [-- Attachment #4: 0001-gnu-Add-ruby-systemu.patch --] [-- Type: text/x-patch, Size: 1670 bytes --] From b7d92cbfd47fa9f4807ea72d570d703b78fb59f7 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft <donttrustben@gmail.com> 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 ^ permalink raw reply related [flat|nested] 5+ messages in thread
* Re: [PATCHES] Update orfm and package test requirements. 2016-01-13 12:48 ` Ben Woodcroft @ 2016-01-13 13:50 ` Ricardo Wurmus 2016-01-13 22:05 ` Ben Woodcroft 0 siblings, 1 reply; 5+ messages in thread From: Ricardo Wurmus @ 2016-01-13 13:50 UTC (permalink / raw) To: Ben Woodcroft; +Cc: guix-devel@gnu.org Ben Woodcroft <b.woodcroft@uq.edu.au> writes: >> “Bio-comandeer lets you run shell commands from within Ruby. ...” > That wasn't the best sentence before, fo so. I wonder if the replacement > is a little bland though. How about (as attached), > > + "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.") This is almost okay, I think. I would add a couple of words to state that messages or text *printed* to STDOUT/STDERR (rather than the streams themselves) are reported. > From b7d92cbfd47fa9f4807ea72d570d703b78fb59f7 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft <donttrustben@gmail.com> > 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. [...] > + (arguments > + `(#:phases > + (modify-phases %standard-phases > + (add-before 'check 'patch-and-set-version > + (lambda _ > + (setenv "VERSION" ,version) > + #t))))) That’s an odd phase name; why “patch”? Is setting the environment variable the only way to set the version or would a make-flag work here, too? (I haven’t checked if the ruby-build-system respects make-flags.) The rest looks good to me. Thanks! ~~ Ricardo ^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCHES] Update orfm and package test requirements. 2016-01-13 13:50 ` Ricardo Wurmus @ 2016-01-13 22:05 ` Ben Woodcroft 0 siblings, 0 replies; 5+ messages in thread From: Ben Woodcroft @ 2016-01-13 22:05 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: guix-devel@gnu.org On 13/01/16 23:50, Ricardo Wurmus wrote: > Ben Woodcroft <b.woodcroft@uq.edu.au> writes: > > [..] >> + (arguments >> + `(#:phases >> + (modify-phases %standard-phases >> + (add-before 'check 'patch-and-set-version >> + (lambda _ >> + (setenv "VERSION" ,version) >> + #t))))) > That’s an odd phase name; why “patch”? Is setting the environment > variable the only way to set the version or would a make-flag work here, > too? (I haven’t checked if the ruby-build-system respects make-flags.) > > The rest looks good to me. Thanks! Pushed, thanks. The phase name above was a bit crufty so I changed it, but had to go with setenv since the ruby-build-system doesn't support make-flags (or rake-flags). Thanks, ben ^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2016-01-13 22:06 UTC | newest] Thread overview: 5+ messages (download: mbox.gz follow: Atom feed -- links below jump to the message on this page -- 2015-11-21 0:45 [PATCHES] Update orfm and package test requirements Ben Woodcroft 2015-11-27 13:19 ` Ricardo Wurmus 2016-01-13 12:48 ` Ben Woodcroft 2016-01-13 13:50 ` Ricardo Wurmus 2016-01-13 22:05 ` Ben Woodcroft
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