Subject: bug#26108: closed (Re: bug#26108: [PATCH 6/7] gnu: Add mia.)

From: [email-masked] (GNU bug Tracking System)
Date: Mon, 15 May 2017 21:10:02 +0000

Your bug report

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

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
26108: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=26108
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: Re: bug#26108: [PATCH 6/7] gnu: Add mia.
From: Ricardo Wurmus <[email-masked]>
To: John Darrington <[email-masked]>
Cc: [email-masked]
Date: Mon, 15 May 2017 23:09:19 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

John Darrington <[email-masked]> 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

Subject: [PATCH 6/7] gnu: Add mia.
From: John Darrington <[email-masked]>
To: [email-masked]
Cc: John Darrington <[email-masked]>
Date: Wed, 15 Mar 2017 21:05:23 +0100
List-Id: <debbugs-submit.debbugs.gnu.org>

* 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" ,[email-masked])))
+    (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