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 address@hidden 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 <address@hidden>
> 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