bug#26108: [PATCH 6/7] gnu: Add mia.

[Ricardo Wurmus <rekado@elephly.net>]

John Darrington <jmd@gnu.org> writes:

> * gnu/packages/image-processing.scm (mia): New variable.
[…]

> +
> +(define-public mia
> +  (package
> +    (name "mia")
> +    (version "2.4.3")
> +    (source (origin
> +              ;; There are too many issues with the released version which
> +              ;; prevent a clean build and test under Guix.  So until the next
> +              ;; release I suggest we use this git checkout.

That’s okay.  Could you please wrap the “(package …)“ expression in a
let expression where ‘commit’ is bound to
"d91cade30a10f179bba8c8e48b84983a296d2c33" and ‘revision’ to "1".  Then
the version field should be changed to

    (string-append "2.4.3-" revision "." (string-take commit 7))

because this is not exactly version "2.4.3”.

> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://git.code.sf.net/p/mia/mia2")
> +                    (commit
> "d91cade30a10f179bba8c8e48b84983a296d2c33")))

After wrapping the thing in a let binding you can use “(commit commit)”
here.

> +              (sha256
> +               (base32
> +                "0y8ihqbliqy21fph3dm5h6k2nvjbajx4y0mn351x990r9y0767vz"))
> +              (file-name (string-append name "-" version))))

Usually, we append “-checkout” to git clones.

> +    (build-system cmake-build-system)
> +    (arguments `(#:configure-flags `("-DMIA_CREATE_NIPYPE_INTERFACES=0"
> +                                     ,(string-append "-DCMAKE_INSTALL_LIBDIR="
> +                                                     (assoc-ref %outputs "out")
> +                                                     "/lib")
> +                                     ;; According to upstream this is necessary
> +                                     ;; with g++-4.9.x because the std::regex
> +                                     ;; library doesn't work reliably.
> +                                     "-DMIA_USE_BOOST_REGEX=ON"
> +
> "-DCMAKE_CXX_FLAGS=-fpermissive")))

I have a slight preference to adding a line break after “arguments”.

> +    (inputs `(("boost" ,boost)
> +              ("dcmtk" ,dcmtk)
> +              ("doxygen" ,doxygen)

I think this should be a native input.

Please also add a line break after “inputs”.

> +              ("eigen" ,eigen)
> +              ("fftw" ,fftw)
> +              ("fftwf" ,fftwf)
> +              ("gsl" ,gsl)
> +              ("gts" ,gts)
> +              ("hdf5" ,hdf5)
> +              ("itpp" ,itpp)
> +              ("libjpeg" ,libjpeg)
> +              ("libpng" ,libpng)
> +              ("libtiff" ,libtiff)
> +              ("libxml" ,libxml2)
> +              ("libxml++" ,libxml++)
> +              ("maxflow" ,maxflow)
> +              ("niftilib" ,niftilib)
> +              ("nlopt" ,nlopt)
> +              ("openexr" ,openexr)
> +              ("python-lxml" ,python2-lxml)
> +              ("vtk" ,vtk@6.3)))
> +    (native-inputs `(("pkg-config"   ,pkg-config)
> +                     ("python" ,python-2)))

Please add a line break after “native-inputs” (for consistency).  Please
also collapse the spaces after "pkg-config".

> +    (synopsis "Toolkit for gray scale medical image analysis")
> +    (description "MIA provides a combination of command line tools, plug-ins,
> +and libraries that make it possible run image processing tasks interactively
> +in a command shell and to prototype using the shell's scripting
> +language.  It is built around a plug-in structure that makes it easy to add
> +functionality without compromising the original code base and it makes use of a
> +wide variety of external libraries that provide additional functionality.")
> +    (home-page "http://mia.sourceforge.net")
> +    (license license:gpl3+)))

The rest looks good to me (I did not check the license).  Would you like
to push an updated version or would you like me to make the changes
myself?

--
Ricardo

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