* bug#26108: [PATCH 6/7] gnu: Add mia. [not found] ` <1489608324-23632-6-git-send-email-jmd@gnu.org> @ 2017-03-30 13:15 ` Ricardo Wurmus 2017-03-31 5:27 ` John Darrington 0 siblings, 1 reply; 6+ messages in thread From: Ricardo Wurmus @ 2017-03-30 13:15 UTC (permalink / raw) To: John Darrington; +Cc: 26108 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 GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net ^ permalink raw reply [flat|nested] 6+ messages in thread
* bug#26108: [PATCH 6/7] gnu: Add mia. 2017-03-30 13:15 ` bug#26108: [PATCH 6/7] gnu: Add mia Ricardo Wurmus @ 2017-03-31 5:27 ` John Darrington 2017-05-15 21:09 ` Ricardo Wurmus 0 siblings, 1 reply; 6+ messages in thread From: John Darrington @ 2017-03-31 5:27 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: 26108 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' ^ permalink raw reply [flat|nested] 6+ messages in thread
* bug#26108: [PATCH 6/7] gnu: Add mia. 2017-03-31 5:27 ` John Darrington @ 2017-05-15 21:09 ` Ricardo Wurmus 0 siblings, 0 replies; 6+ messages in thread From: Ricardo Wurmus @ 2017-05-15 21:09 UTC (permalink / raw) To: John Darrington; +Cc: 26108-done John Darrington <jmd@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 ^ permalink raw reply [flat|nested] 6+ messages in thread
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* bug#26111: [PATCH 5/7] gnu: Add vtk version 6.3.0 [not found] ` <1489608324-23632-5-git-send-email-jmd@gnu.org> @ 2017-05-11 6:44 ` Ricardo Wurmus 0 siblings, 0 replies; 6+ messages in thread From: Ricardo Wurmus @ 2017-05-11 6:44 UTC (permalink / raw) To: John Darrington; +Cc: 26111-done John Darrington <jmd@gnu.org> writes: > * gnu/packages/vtk.scm (vtk@6.3): New variable. > --- […] > +;; Mia 2.4.3 doesn't work against vtk7 so we package vtk 6.3 for it: Meanwhile Mia 2.4.4 has been released which is compatible with vtk7, so I’m closing this bug. I’m currently working on this patch set and have updated dcmtk and mia. I’ll push them once I’ve confirmed they are working correctly. Thanks! -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net ^ permalink raw reply [flat|nested] 6+ messages in thread
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* bug#26109: [PATCH 3/7] gnu: Add dcmtk. [not found] ` <20170321183012.GC28482@jasmine> @ 2017-05-15 21:07 ` Ricardo Wurmus 0 siblings, 0 replies; 6+ messages in thread From: Ricardo Wurmus @ 2017-05-15 21:07 UTC (permalink / raw) To: Leo Famulari; +Cc: 26109-done, John Darrington Leo Famulari <leo@famulari.name> writes: >> Or, we could try building from an arbitrary Git commit. >> >> Yes. That is the other option - I think it might be a what we'll have to do. > > Okay, let us know how it goes. I tried extracting a patch but it was virtually impossible to make it apply without introducing more security problems in the attempt. So I updated the package to use the latest commit from git. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net ^ permalink raw reply [flat|nested] 6+ messages in thread
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* bug#26110: [PATCH 7/7] gnu: Move vtk to image-processing.scm [not found] ` <1489608324-23632-7-git-send-email-jmd@gnu.org> @ 2017-06-02 16:31 ` Ludovic Courtès 0 siblings, 0 replies; 6+ messages in thread From: Ludovic Courtès @ 2017-06-02 16:31 UTC (permalink / raw) To: John Darrington; +Cc: 26110-done John Darrington <jmd@gnu.org> skribis: > * gnu/packages/image-processing.scm (vtk, vtk@6.3): New variables. > * gnu/packages/vtk.scm: Delete file. > * gnu/local.mk (GNU_SYSTEM_MODULES)[gnu/packages/vtk.scm]: Remove. Applied, thanks John! Ludo'. ^ permalink raw reply [flat|nested] 6+ messages in thread
end of thread, other threads:[~2017-06-02 16:33 UTC | newest] Thread overview: 6+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- [not found] <1489608324-23632-1-git-send-email-jmd@gnu.org> [not found] ` <1489608324-23632-6-git-send-email-jmd@gnu.org> 2017-03-30 13:15 ` bug#26108: [PATCH 6/7] gnu: Add mia Ricardo Wurmus 2017-03-31 5:27 ` John Darrington 2017-05-15 21:09 ` Ricardo Wurmus [not found] ` <1489608324-23632-5-git-send-email-jmd@gnu.org> 2017-05-11 6:44 ` bug#26111: [PATCH 5/7] gnu: Add vtk version 6.3.0 Ricardo Wurmus [not found] ` <1489608324-23632-3-git-send-email-jmd@gnu.org> [not found] ` <871stv7hyk.fsf@openmailbox.org> [not found] ` <20170318072335.GA12217@jocasta.intra> [not found] ` <20170321021240.GA29321@jasmine> [not found] ` <20170321023043.GA455@jocasta.intra> [not found] ` <20170321183012.GC28482@jasmine> 2017-05-15 21:07 ` bug#26109: [PATCH 3/7] gnu: Add dcmtk Ricardo Wurmus [not found] ` <1489608324-23632-7-git-send-email-jmd@gnu.org> 2017-06-02 16:31 ` bug#26110: [PATCH 7/7] gnu: Move vtk to image-processing.scm Ludovic Courtès
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