[Debian-med-packaging] r22824 - in trunk/packages/invesalius/trunk/debian: . patches
Thiago Franco Moraes
tfmoraes at cti.gov.br
Tue Nov 8 18:23:00 UTC 2016
Hi Andreas,
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. Sorry if I behave incorrectly.
The problem is with Skimage, isn't it?
Kind regards.
Thiago.
On Tue, Nov 8, 2016 at 3:58 PM Andreas Tille <andreas at an3as.eu> wrote:
> Hi Thiago,
>
> I'm always wondering whether invesalius is ready for upload or not. I
> hope you'll remember that it needs an extra ping if you want me to
> upload - otherwise the packaging will idle in SVN without any action.
>
> BTW, due to this bug
>
> https://bugs.debian.org/840589
>
> invesalius currently does not migrate to Debian testing. If you want
> to make sure invesalius will be part of the next stable Debian release
> it might be sensible to help fixing this bug.
>
> Kind regards
>
> Andreas.
>
> On Thu, Oct 06, 2016 at 02:28:31PM +0000, Thiago Franco Moraes wrote:
> > Author: tfmoraes-guest
> > Date: 2016-10-06 14:28:25 +0000 (Thu, 06 Oct 2016)
> > New Revision: 22824
> >
> > Added:
> >
> trunk/packages/invesalius/trunk/debian/patches/10_import_cython_modules.patch
> > Modified:
> > trunk/packages/invesalius/trunk/debian/invesalius-bin.install
> > trunk/packages/invesalius/trunk/debian/patches/series
> > trunk/packages/invesalius/trunk/debian/rules
> > Log:
> > Compiling cython modules to /usr/bin/invesalius/invesalius_cy
> >
> > Modified: trunk/packages/invesalius/trunk/debian/invesalius-bin.install
> > ===================================================================
> > --- trunk/packages/invesalius/trunk/debian/invesalius-bin.install
> 2016-10-03 16:43:53 UTC (rev 22823)
> > +++ trunk/packages/invesalius/trunk/debian/invesalius-bin.install
> 2016-10-06 14:28:25 UTC (rev 22824)
> > @@ -1 +1,2 @@
> > -invesalius/data/*.so /usr/share/invesalius/invesalius/data/
> > +invesalius_cy/*.py /usr/lib/invesalius/invesalius_cy/
> > +invesalius_cy/*.so /usr/lib/invesalius/invesalius_cy/
> >
> > Added:
> trunk/packages/invesalius/trunk/debian/patches/10_import_cython_modules.patch
> > ===================================================================
> > ---
> trunk/packages/invesalius/trunk/debian/patches/10_import_cython_modules.patch
> (rev 0)
> > +++
> trunk/packages/invesalius/trunk/debian/patches/10_import_cython_modules.patch
> 2016-10-06 14:28:25 UTC (rev 22824)
> > @@ -0,0 +1,77 @@
> > +Author: Thiago Franco de Moraes
> > +Date: Thu, 06 Oct 2016 11:22:46 -0200
> > +Description: Moving cython compiled modules to /usr/lib/invesalius
> folder and
> > +adapts invesalius to run this way.
> > +diff --git a/invesalius/data/mask.py b/invesalius/data/mask.py
> > +index d00d22e..be9423a 100644
> > +--- a/invesalius/data/mask.py
> > ++++ b/invesalius/data/mask.py
> > +@@ -30,7 +30,7 @@ import invesalius.constants as const
> > + import invesalius.data.imagedata_utils as iu
> > + import invesalius.session as ses
> > +
> > +-from . import floodfill
> > ++from invesalius_cy import floodfill
> > +
> > + from wx.lib.pubsub import pub as Publisher
> > + from scipy import ndimage
> > +diff --git a/invesalius/data/slice_.py b/invesalius/data/slice_.py
> > +index 65433bb..07d9eff 100644
> > +--- a/invesalius/data/slice_.py
> > ++++ b/invesalius/data/slice_.py
> > +@@ -31,9 +31,9 @@ import invesalius.session as ses
> > + import invesalius.utils as utils
> > + from invesalius.data.mask import Mask
> > + from invesalius.project import Project
> > +-from invesalius.data import mips
> > ++from invesalius_cy import mips
> > +
> > +-from invesalius.data import transforms
> > ++from invesalius_cy import transforms
> > + import invesalius.data.transformations as transformations
> > + OTHER=0
> > + PLIST=1
> > +diff --git a/invesalius/data/styles.py b/invesalius/data/styles.py
> > +index c82ba40..5cfeac5 100644
> > +--- a/invesalius/data/styles.py
> > ++++ b/invesalius/data/styles.py
> > +@@ -46,7 +46,7 @@ from skimage import filter
> > + import invesalius.gui.dialogs as dialogs
> > + from invesalius.data.measures import MeasureData
> > +
> > +-from . import floodfill
> > ++from invesalius_cy import floodfill
> > +
> > + import invesalius.data.watershed_process as watershed_process
> > + import invesalius.utils as utils
> > +diff --git a/setup.py b/setup.py
> > +index c9223db..c466a29 100644
> > +--- a/setup.py
> > ++++ b/setup.py
> > +@@ -11,22 +11,22 @@ import numpy
> > + if sys.platform == 'linux2':
> > + setup(
> > + cmdclass = {'build_ext': build_ext},
> > +- ext_modules = cythonize([ Extension("invesalius.data.mips",
> ["invesalius/data/mips.pyx"],
> > ++ ext_modules = cythonize([ Extension("invesalius_cy.mips",
> ["invesalius_cy/mips.pyx"],
> > + include_dirs =
> [numpy.get_include()],
> > + extra_compile_args=['-fopenmp'],
> > + extra_link_args=['-fopenmp']),
> > +
> > +- Extension("invesalius.data.interpolation",
> ["invesalius/data/interpolation.pyx"],
> > ++ Extension("invesalius_cy.interpolation",
> ["invesalius_cy/interpolation.pyx"],
> > + include_dirs=[numpy.get_include()],
> > + extra_compile_args=['-fopenmp',],
> > + extra_link_args=['-fopenmp',]),
> > +
> > +- Extension("invesalius.data.transforms",
> ["invesalius/data/transforms.pyx"],
> > ++ Extension("invesalius_cy.transforms",
> ["invesalius_cy/transforms.pyx"],
> > + include_dirs=[numpy.get_include()],
> > + extra_compile_args=['-fopenmp',],
> > + extra_link_args=['-fopenmp',]),
> > +
> > +- Extension("invesalius.data.floodfill",
> ["invesalius/data/floodfill.pyx"],
> > ++ Extension("invesalius_cy.floodfill",
> ["invesalius_cy/floodfill.pyx"],
> > + include_dirs=[numpy.get_include()],
> > + language='c++',),
> > + ])
> >
> > Modified: trunk/packages/invesalius/trunk/debian/patches/series
> > ===================================================================
> > --- trunk/packages/invesalius/trunk/debian/patches/series 2016-10-03
> 16:43:53 UTC (rev 22823)
> > +++ trunk/packages/invesalius/trunk/debian/patches/series 2016-10-06
> 14:28:25 UTC (rev 22824)
> > @@ -1 +1,2 @@
> > 10_sample_path.patch
> > +10_import_cython_modules.patch
> >
> > Modified: trunk/packages/invesalius/trunk/debian/rules
> > ===================================================================
> > --- trunk/packages/invesalius/trunk/debian/rules 2016-10-03
> 16:43:53 UTC (rev 22823)
> > +++ trunk/packages/invesalius/trunk/debian/rules 2016-10-06
> 14:28:25 UTC (rev 22824)
> > @@ -19,15 +19,22 @@
> > override_dh_auto_build:
> > python setup.py build_ext --inplace
> >
> > -override_dh_auto_clean:
> > +override_dh_auto_clean: create-cython-dir
> > dh_auto_clean
> > rm -f invesalius-3.0
> >
> > -override_dh_compress :
> > +override_dh_compress:
> > dh_compress --exclude=LICENSE.pt.txt --exclude=.inv3
> >
> > +create-cython-dir:
> > + mkdir invesalius_cy/
> > + touch invesalius_cy/__init__.py
> > + cp invesalius/data/*.pyx invesalius_cy
> > + cp invesalius/data/*.pxd invesalius_cy
> > +
> > create-launcher:
> > echo '#!/bin/sh' > invesalius-3.0
> > + echo 'export PYTHONPATH=$$PYTHONPATH:"/usr/lib/invesalius"' >>
> invesalius-3.0
> > echo 'export INVESALIUS_LIBRARY_PATH="/usr/share/invesalius/"' >>
> invesalius-3.0
> > echo 'cd $$INVESALIUS_LIBRARY_PATH' >> invesalius-3.0
> > echo 'python app.py $$@' >> invesalius-3.0
> >
> >
> > _______________________________________________
> > debian-med-commit mailing list
> > debian-med-commit at lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
> >
>
> --
> http://fam-tille.de
>
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