<div dir="ltr"><div><div><div><div>Hi Andreas,<br><br></div>We are now working in a new InVesalius version. This commit to the debian package is just to adapt to the new (3.1, unstable yet) invesalius version. I was only antecipating the changes to make the package to version we are going to release soon.<span id="inbox-inbox-result_box" class="inbox-inbox-short_text" lang="en"><span class="inbox-inbox-"> Sorry if I behave incorrectly.<br><br></span></span></div><span id="inbox-inbox-result_box" class="inbox-inbox-short_text" lang="en"><span class="inbox-inbox-">The problem is with Skimage, isn't it?<br><br></span></span></div><span id="inbox-inbox-result_box" class="inbox-inbox-short_text" lang="en"><span class="inbox-inbox-">Kind regards.<br></span></span></div><span id="inbox-inbox-result_box" class="inbox-inbox-short_text" lang="en"><span class="inbox-inbox-">Thiago.<br></span></span><div><div><div><div><div><div><br><div class="gmail_quote"><div dir="ltr">On Tue, Nov 8, 2016 at 3:58 PM Andreas Tille <<a href="mailto:andreas@an3as.eu">andreas@an3as.eu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Thiago,<br class="gmail_msg">
<br class="gmail_msg">
I'm always wondering whether invesalius is ready for upload or not. I<br class="gmail_msg">
hope you'll remember that it needs an extra ping if you want me to<br class="gmail_msg">
upload - otherwise the packaging will idle in SVN without any action.<br class="gmail_msg">
<br class="gmail_msg">
BTW, due to this bug<br class="gmail_msg">
<br class="gmail_msg">
<a href="https://bugs.debian.org/840589" rel="noreferrer" class="gmail_msg" target="_blank">https://bugs.debian.org/840589</a><br class="gmail_msg">
<br class="gmail_msg">
invesalius currently does not migrate to Debian testing. If you want<br class="gmail_msg">
to make sure invesalius will be part of the next stable Debian release<br class="gmail_msg">
it might be sensible to help fixing this bug.<br class="gmail_msg">
<br class="gmail_msg">
Kind regards<br class="gmail_msg">
<br class="gmail_msg">
Andreas.<br class="gmail_msg">
<br class="gmail_msg">
On Thu, Oct 06, 2016 at 02:28:31PM +0000, Thiago Franco Moraes wrote:<br class="gmail_msg">
> Author: tfmoraes-guest<br class="gmail_msg">
> Date: 2016-10-06 14:28:25 +0000 (Thu, 06 Oct 2016)<br class="gmail_msg">
> New Revision: 22824<br class="gmail_msg">
><br class="gmail_msg">
> Added:<br class="gmail_msg">
> trunk/packages/invesalius/trunk/debian/patches/10_import_cython_modules.patch<br class="gmail_msg">
> Modified:<br class="gmail_msg">
> trunk/packages/invesalius/trunk/debian/invesalius-bin.install<br class="gmail_msg">
> trunk/packages/invesalius/trunk/debian/patches/series<br class="gmail_msg">
> trunk/packages/invesalius/trunk/debian/rules<br class="gmail_msg">
> Log:<br class="gmail_msg">
> Compiling cython modules to /usr/bin/invesalius/invesalius_cy<br class="gmail_msg">
><br class="gmail_msg">
> Modified: trunk/packages/invesalius/trunk/debian/invesalius-bin.install<br class="gmail_msg">
> ===================================================================<br class="gmail_msg">
> --- trunk/packages/invesalius/trunk/debian/invesalius-bin.install 2016-10-03 16:43:53 UTC (rev 22823)<br class="gmail_msg">
> +++ trunk/packages/invesalius/trunk/debian/invesalius-bin.install 2016-10-06 14:28:25 UTC (rev 22824)<br class="gmail_msg">
> @@ -1 +1,2 @@<br class="gmail_msg">
> -invesalius/data/*.so /usr/share/invesalius/invesalius/data/<br class="gmail_msg">
> +invesalius_cy/*.py /usr/lib/invesalius/invesalius_cy/<br class="gmail_msg">
> +invesalius_cy/*.so /usr/lib/invesalius/invesalius_cy/<br class="gmail_msg">
><br class="gmail_msg">
> Added: trunk/packages/invesalius/trunk/debian/patches/10_import_cython_modules.patch<br class="gmail_msg">
> ===================================================================<br class="gmail_msg">
> --- trunk/packages/invesalius/trunk/debian/patches/10_import_cython_modules.patch (rev 0)<br class="gmail_msg">
> +++ trunk/packages/invesalius/trunk/debian/patches/10_import_cython_modules.patch 2016-10-06 14:28:25 UTC (rev 22824)<br class="gmail_msg">
> @@ -0,0 +1,77 @@<br class="gmail_msg">
> +Author: Thiago Franco de Moraes<br class="gmail_msg">
> +Date: Thu, 06 Oct 2016 11:22:46 -0200<br class="gmail_msg">
> +Description: Moving cython compiled modules to /usr/lib/invesalius folder and<br class="gmail_msg">
> +adapts invesalius to run this way.<br class="gmail_msg">
> +diff --git a/invesalius/data/mask.py b/invesalius/data/mask.py<br class="gmail_msg">
> +index d00d22e..be9423a 100644<br class="gmail_msg">
> +--- a/invesalius/data/mask.py<br class="gmail_msg">
> ++++ b/invesalius/data/mask.py<br class="gmail_msg">
> +@@ -30,7 +30,7 @@ import invesalius.constants as const<br class="gmail_msg">
> + import invesalius.data.imagedata_utils as iu<br class="gmail_msg">
> + import invesalius.session as ses<br class="gmail_msg">
> +<br class="gmail_msg">
> +-from . import floodfill<br class="gmail_msg">
> ++from invesalius_cy import floodfill<br class="gmail_msg">
> +<br class="gmail_msg">
> + from wx.lib.pubsub import pub as Publisher<br class="gmail_msg">
> + from scipy import ndimage<br class="gmail_msg">
> +diff --git a/invesalius/data/slice_.py b/invesalius/data/slice_.py<br class="gmail_msg">
> +index 65433bb..07d9eff 100644<br class="gmail_msg">
> +--- a/invesalius/data/slice_.py<br class="gmail_msg">
> ++++ b/invesalius/data/slice_.py<br class="gmail_msg">
> +@@ -31,9 +31,9 @@ import invesalius.session as ses<br class="gmail_msg">
> + import invesalius.utils as utils<br class="gmail_msg">
> + from invesalius.data.mask import Mask<br class="gmail_msg">
> + from invesalius.project import Project<br class="gmail_msg">
> +-from invesalius.data import mips<br class="gmail_msg">
> ++from invesalius_cy import mips<br class="gmail_msg">
> +<br class="gmail_msg">
> +-from invesalius.data import transforms<br class="gmail_msg">
> ++from invesalius_cy import transforms<br class="gmail_msg">
> + import invesalius.data.transformations as transformations<br class="gmail_msg">
> + OTHER=0<br class="gmail_msg">
> + PLIST=1<br class="gmail_msg">
> +diff --git a/invesalius/data/styles.py b/invesalius/data/styles.py<br class="gmail_msg">
> +index c82ba40..5cfeac5 100644<br class="gmail_msg">
> +--- a/invesalius/data/styles.py<br class="gmail_msg">
> ++++ b/invesalius/data/styles.py<br class="gmail_msg">
> +@@ -46,7 +46,7 @@ from skimage import filter<br class="gmail_msg">
> + import invesalius.gui.dialogs as dialogs<br class="gmail_msg">
> + from invesalius.data.measures import MeasureData<br class="gmail_msg">
> +<br class="gmail_msg">
> +-from . import floodfill<br class="gmail_msg">
> ++from invesalius_cy import floodfill<br class="gmail_msg">
> +<br class="gmail_msg">
> + import invesalius.data.watershed_process as watershed_process<br class="gmail_msg">
> + import invesalius.utils as utils<br class="gmail_msg">
> +diff --git a/setup.py b/setup.py<br class="gmail_msg">
> +index c9223db..c466a29 100644<br class="gmail_msg">
> +--- a/setup.py<br class="gmail_msg">
> ++++ b/setup.py<br class="gmail_msg">
> +@@ -11,22 +11,22 @@ import numpy<br class="gmail_msg">
> + if sys.platform == 'linux2':<br class="gmail_msg">
> + setup(<br class="gmail_msg">
> + cmdclass = {'build_ext': build_ext},<br class="gmail_msg">
> +- ext_modules = cythonize([ Extension("invesalius.data.mips", ["invesalius/data/mips.pyx"],<br class="gmail_msg">
> ++ ext_modules = cythonize([ Extension("invesalius_cy.mips", ["invesalius_cy/mips.pyx"],<br class="gmail_msg">
> + include_dirs = [numpy.get_include()],<br class="gmail_msg">
> + extra_compile_args=['-fopenmp'],<br class="gmail_msg">
> + extra_link_args=['-fopenmp']),<br class="gmail_msg">
> +<br class="gmail_msg">
> +- Extension("invesalius.data.interpolation", ["invesalius/data/interpolation.pyx"],<br class="gmail_msg">
> ++ Extension("invesalius_cy.interpolation", ["invesalius_cy/interpolation.pyx"],<br class="gmail_msg">
> + include_dirs=[numpy.get_include()],<br class="gmail_msg">
> + extra_compile_args=['-fopenmp',],<br class="gmail_msg">
> + extra_link_args=['-fopenmp',]),<br class="gmail_msg">
> +<br class="gmail_msg">
> +- Extension("invesalius.data.transforms", ["invesalius/data/transforms.pyx"],<br class="gmail_msg">
> ++ Extension("invesalius_cy.transforms", ["invesalius_cy/transforms.pyx"],<br class="gmail_msg">
> + include_dirs=[numpy.get_include()],<br class="gmail_msg">
> + extra_compile_args=['-fopenmp',],<br class="gmail_msg">
> + extra_link_args=['-fopenmp',]),<br class="gmail_msg">
> +<br class="gmail_msg">
> +- Extension("invesalius.data.floodfill", ["invesalius/data/floodfill.pyx"],<br class="gmail_msg">
> ++ Extension("invesalius_cy.floodfill", ["invesalius_cy/floodfill.pyx"],<br class="gmail_msg">
> + include_dirs=[numpy.get_include()],<br class="gmail_msg">
> + language='c++',),<br class="gmail_msg">
> + ])<br class="gmail_msg">
><br class="gmail_msg">
> Modified: trunk/packages/invesalius/trunk/debian/patches/series<br class="gmail_msg">
> ===================================================================<br class="gmail_msg">
> --- trunk/packages/invesalius/trunk/debian/patches/series 2016-10-03 16:43:53 UTC (rev 22823)<br class="gmail_msg">
> +++ trunk/packages/invesalius/trunk/debian/patches/series 2016-10-06 14:28:25 UTC (rev 22824)<br class="gmail_msg">
> @@ -1 +1,2 @@<br class="gmail_msg">
> 10_sample_path.patch<br class="gmail_msg">
> +10_import_cython_modules.patch<br class="gmail_msg">
><br class="gmail_msg">
> Modified: trunk/packages/invesalius/trunk/debian/rules<br class="gmail_msg">
> ===================================================================<br class="gmail_msg">
> --- trunk/packages/invesalius/trunk/debian/rules 2016-10-03 16:43:53 UTC (rev 22823)<br class="gmail_msg">
> +++ trunk/packages/invesalius/trunk/debian/rules 2016-10-06 14:28:25 UTC (rev 22824)<br class="gmail_msg">
> @@ -19,15 +19,22 @@<br class="gmail_msg">
> override_dh_auto_build:<br class="gmail_msg">
> python setup.py build_ext --inplace<br class="gmail_msg">
><br class="gmail_msg">
> -override_dh_auto_clean:<br class="gmail_msg">
> +override_dh_auto_clean: create-cython-dir<br class="gmail_msg">
> dh_auto_clean<br class="gmail_msg">
> rm -f invesalius-3.0<br class="gmail_msg">
><br class="gmail_msg">
> -override_dh_compress :<br class="gmail_msg">
> +override_dh_compress:<br class="gmail_msg">
> dh_compress --exclude=LICENSE.pt.txt --exclude=.inv3<br class="gmail_msg">
><br class="gmail_msg">
> +create-cython-dir:<br class="gmail_msg">
> + mkdir invesalius_cy/<br class="gmail_msg">
> + touch invesalius_cy/__init__.py<br class="gmail_msg">
> + cp invesalius/data/*.pyx invesalius_cy<br class="gmail_msg">
> + cp invesalius/data/*.pxd invesalius_cy<br class="gmail_msg">
> +<br class="gmail_msg">
> create-launcher:<br class="gmail_msg">
> echo '#!/bin/sh' > invesalius-3.0<br class="gmail_msg">
> + echo 'export PYTHONPATH=$$PYTHONPATH:"/usr/lib/invesalius"' >> invesalius-3.0<br class="gmail_msg">
> echo 'export INVESALIUS_LIBRARY_PATH="/usr/share/invesalius/"' >> invesalius-3.0<br class="gmail_msg">
> echo 'cd $$INVESALIUS_LIBRARY_PATH' >> invesalius-3.0<br class="gmail_msg">
> echo 'python app.py $$@' >> invesalius-3.0<br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
> _______________________________________________<br class="gmail_msg">
> debian-med-commit mailing list<br class="gmail_msg">
> <a href="mailto:debian-med-commit@lists.alioth.debian.org" class="gmail_msg" target="_blank">debian-med-commit@lists.alioth.debian.org</a><br class="gmail_msg">
> <a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit" rel="noreferrer" class="gmail_msg" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit</a><br class="gmail_msg">
><br class="gmail_msg">
<br class="gmail_msg">
--<br class="gmail_msg">
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</blockquote></div></div></div></div></div></div></div></div>