GNU bug report logs - #26108
[PATCH 6/7] gnu: Add mia.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: John Darrington <jmd <at> gnu.org>
To: guix-patches <at> gnu.org
Cc: John Darrington <jmd <at> gnu.org>
Subject: [PATCH 6/7] gnu: Add mia.
Date: Wed, 15 Mar 2017 21:05:23 +0100

* gnu/packages/image-processing.scm (mia): New variable.
---
 gnu/packages/image-processing.scm | 75 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 74 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index e1ad93e..e080569 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -21,12 +21,25 @@
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cmake)
   #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages gnome)
+  #:use-module (gnu packages graphics)
+  #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages xml)
   #:use-module (gnu packages image)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages tbb)
+  #:use-module (gnu packages vtk))
 
 (define-public dcmtk
   (package
@@ -73,3 +86,63 @@ demonstrative image storage and worklist servers.")
               "file://COPYRIGHT"
               "A union of the Apache 2.0 licence and various non-copyleft
 licences similar to the Modified BSD licence."))))
+
+
+(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.
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://git.code.sf.net/p/mia/mia2")
+                    (commit "d91cade30a10f179bba8c8e48b84983a296d2c33")))
+              (sha256
+               (base32
+                "0y8ihqbliqy21fph3dm5h6k2nvjbajx4y0mn351x990r9y0767vz"))
+              (file-name (string-append name "-" version))))
+    (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")))
+    (inputs `(("boost" ,boost)
+              ("dcmtk" ,dcmtk)
+              ("doxygen" ,doxygen)
+              ("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 <at> 6.3)))
+    (native-inputs `(("pkg-config"   ,pkg-config)
+                     ("python" ,python-2)))
+    (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+)))
-- 
2.1.4

Message #8 received at 26108 <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kei <at> openmailbox.org>
To: John Darrington <jmd <at> gnu.org>
Cc: 26108 <at> debbugs.gnu.org
Subject: Re: bug#26108: [PATCH 6/7] gnu: Add mia.
Date: Sat, 18 Mar 2017 01:53:42 -0400

[Message part 1 (text/plain, inline)]

John Darrington <jmd <at> gnu.org> writes:

> * gnu/packages/image-processing.scm (mia): New variable.
> ---
>  gnu/packages/image-processing.scm | 75 ++++++++++++++++++++++++++++++++++++++-
>  1 file changed, 74 insertions(+), 1 deletion(-)
>
> diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
> index e1ad93e..e080569 100644
> --- a/gnu/packages/image-processing.scm
> +++ b/gnu/packages/image-processing.scm
> @@ -21,12 +21,25 @@
>    #:use-module (guix packages)
>    #:use-module (guix utils)
>    #:use-module (guix download)
> +  #:use-module (guix git-download)
>    #:use-module (guix build-system gnu)
> +  #:use-module (guix build-system cmake)
>    #:use-module (gnu packages)
> +  #:use-module (gnu packages algebra)
> +  #:use-module (gnu packages boost)
>    #:use-module (gnu packages compression)
>    #:use-module (gnu packages documentation)
> +  #:use-module (gnu packages gnome)
> +  #:use-module (gnu packages graphics)
> +  #:use-module (gnu packages graphviz)
> +  #:use-module (gnu packages maths)
> +  #:use-module (gnu packages xml)
>    #:use-module (gnu packages image)
> -  #:use-module (gnu packages perl))
> +  #:use-module (gnu packages perl)
> +  #:use-module (gnu packages pkg-config)
> +  #:use-module (gnu packages python)
> +  #:use-module (gnu packages tbb)
> +  #:use-module (gnu packages vtk))
>  
>  (define-public dcmtk
>    (package
> @@ -73,3 +86,63 @@ demonstrative image storage and worklist servers.")
>                "file://COPYRIGHT"
>                "A union of the Apache 2.0 licence and various non-copyleft
>  licences similar to the Modified BSD licence."))))
> +
> +
> +(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.
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://git.code.sf.net/p/mia/mia2")
> +                    (commit "d91cade30a10f179bba8c8e48b84983a296d2c33")))
> +              (sha256
> +               (base32
> +                "0y8ihqbliqy21fph3dm5h6k2nvjbajx4y0mn351x990r9y0767vz"))
> +              (file-name (string-append name "-" version))))
> +    (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")))
> +    (inputs `(("boost" ,boost)
> +              ("dcmtk" ,dcmtk)
> +              ("doxygen" ,doxygen)
> +              ("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 <at> 6.3)))
> +    (native-inputs `(("pkg-config"   ,pkg-config)
> +                     ("python" ,python-2)))
> +    (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+)))

My machine doesn't have the hardware to build this package in a
reasonable amount of time, but it lints file and looks good!

[signature.asc (application/pgp-signature, inline)]

Message #11 received at 26108 <at> debbugs.gnu.org (full text, mbox):

From: John Darrington <john <at> darrington.wattle.id.au>
To: Kei Kebreau <kei <at> openmailbox.org>
Cc: 26108 <at> debbugs.gnu.org, John Darrington <jmd <at> gnu.org>
Subject: Re: bug#26108: [PATCH 6/7] gnu: Add mia.
Date: Sat, 18 Mar 2017 07:17:23 +0100

[Message part 1 (text/plain, inline)]

On Sat, Mar 18, 2017 at 01:53:42AM -0400, Kei Kebreau wrote:
     
     My machine doesn't have the hardware to build this package in a
     reasonable amount of time, but it lints file and looks good!

Yeah.  It takes about an hour for me.

Thanks for the reviews anyway.

J'


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Message #14 received at 26108 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: John Darrington <jmd <at> gnu.org>
Cc: 26108 <at> debbugs.gnu.org
Subject: Re: bug#26108: [PATCH 6/7] gnu: Add mia.
Date: Thu, 30 Mar 2017 15:15:51 +0200

John Darrington <jmd <at> 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 <at> 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

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Message #17 received at 26108 <at> debbugs.gnu.org (full text, mbox):

From: John Darrington <jmd <at> gnu.org>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 26108 <at> debbugs.gnu.org
Subject: Re: bug#26108: [PATCH 6/7] gnu: Add mia.
Date: Fri, 31 Mar 2017 01:27:54 -0400

On Thu, Mar 30, 2017 at 03:15:51PM +0200, Ricardo Wurmus wrote:
> 
> > +    (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?

Feel free to make any changes you think necessary and commit it if appropriate.

J'

Message #22 received at 26108-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: John Darrington <jmd <at> gnu.org>
Cc: 26108-done <at> debbugs.gnu.org
Subject: Re: bug#26108: [PATCH 6/7] gnu: Add mia.
Date: Mon, 15 May 2017 23:09:19 +0200

John Darrington <jmd <at> gnu.org> writes:

> On Thu, Mar 30, 2017 at 03:15:51PM +0200, Ricardo Wurmus wrote:
>>
>> > +    (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?
>
> Feel free to make any changes you think necessary and commit it if appropriate.

I made some changes, updated to the latest version, and pushed it to
master.

Thank you, John, for the patch, and my apologies for letting it sit here
for so long!  (It was impossible to build it on my laptop, so I had to
arrange for a different machine.)

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

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