[PATCHES] Update orfm and package test requirements.

[PATCHES] Update orfm and package test requirements.

[Ben Woodcroft]

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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

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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


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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


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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

Re: [PATCHES] Update orfm and package test requirements.

[Ricardo Wurmus]

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

Re: [PATCHES] Update orfm and package test requirements.

[Ben Woodcroft]

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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


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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


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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


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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

Re: [PATCHES] Update orfm and package test requirements.

[Ricardo Wurmus]

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

Re: [PATCHES] Update orfm and package test requirements.

[Ben Woodcroft]

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