Package Details: python-scikit-image 0.19.3-1

Git Clone URL: https://aur.archlinux.org/python-scikit-image.git (read-only, click to copy)
Package Base: python-scikit-image
Description: Image processing routines for SciPy
Upstream URL: http://scikit-image.org
Licenses: BSD
Submitter: Dragonlord
Maintainer: Universebenzene
Last Packager: Universebenzene
Votes: 63
Popularity: 0.38
First Submitted: 2016-04-30 10:32 (UTC)
Last Updated: 2022-06-24 08:01 (UTC)

Latest Comments

Moebius14 commented on 2022-06-24 03:19 (UTC)

I got no such file error when it tries to create symbolic links.

The solution was to change line 67 in the PKGBUILD to:

    for _pyso in build/lib.linux-${CARCH}-cpython-${_pyver/./}/skimage/*/*cpython-${_pyver/./}-${CARCH}-linux-gnu.so; do

VorpalGun commented on 2022-06-10 13:12 (UTC)

I believe the PKGBUILD can at least be fixed to pass -j with a numeric value extracted from $MAKEFLAGS to build_ext (as it also seems to build single threaded), I'm less sure of how to properly fix distcc support though.

carlosal1015 commented on 2022-06-08 19:48 (UTC)

@VorpalGun, maybe you want to try arch4edu.

arch4edu/python-scikit-image 0.19.2-1
    Image processing routines for SciPy

I saw some pytests are not passing. Compilation is fine.

VorpalGun commented on 2022-06-08 18:25 (UTC)

Building with distcc seems broken for this package. It completely ignores distcc. And it takes a long time to build as well :(

trougnouf commented on 2021-12-30 10:50 (UTC) (edited on 2021-12-30 10:51 (UTC) by trougnouf)

I updated and adopted python-pythran-git.

edit: I didn't realize python-pythran is in the official repository. I don't know why pacaur was throwing this error.

trougnouf commented on 2021-12-30 10:31 (UTC) (edited on 2021-12-30 10:34 (UTC) by trougnouf)

Missing dependency: python-pythran . Here is the last PKGBUILD before the package was removed: https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=python-pythran-git

maverick1 commented on 2021-06-09 08:25 (UTC)

I think it is better to switch to this URL https://github.com/scikit-image/scikit-image/archive/refs/tags/v0.18.1.tar.gz

daniel_shub commented on 2021-03-18 14:25 (UTC)

The python-setuptools package is pulled in by python-coverage which is pulled in by python-pytest-cov. The python-pytest-cov is in checkdepends, but not makedepends. I think this means makepkg will fail with the --nocheck option. The PKGBUILD guideline wiki (https://wiki.archlinux.org/index.php/Arch_package_guidelines) doesn't cover what to do in this case and namcap is useless for Python packages so I asked in the forums: https://bbs.archlinux.org/viewtopic.php?pid=1962482#p1962482

CyberShadow commented on 2021-03-18 07:15 (UTC)

==> Starting build()...
Traceback (most recent call last):
  File "/build/python-scikit-image/src/scikit-image-0.18.1/setup.py", line 10, in <module>
    import setuptools
ModuleNotFoundError: No module named 'setuptools'

Missing dependency to python-setuptools?

Universebenzene commented on 2021-02-10 02:21 (UTC)

@selion python-pywavelets is already in depends. I don't know why you get this problem. And also I don't know why you created a deletion request.

selion commented on 2021-02-09 22:48 (UTC) (edited on 2021-02-09 22:49 (UTC) by selion)

I get a module not found error pywt when importing skimage.filters

Installing python-pywavelets fixes that

ricot commented on 2020-10-27 11:18 (UTC)

Build seems to only use a single CPU core and hence is excruciatingly slow. Any chance we could use multiple cores?

df8oe commented on 2020-06-23 10:42 (UTC)

No install possible - what is the problem?
======================================================================================= short test summary info ======================================================================================= FAILED skimage/color/tests/test_colorconv.py::TestColorconv::test_lab_full_gamut - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current re... FAILED skimage/color/tests/test_colorconv.py::TestColorconv::test_rgb2gray_alpha - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current re... FAILED skimage/color/tests/test_colorconv.py::test_nD_gray_conversion[shape0-rgb2gray] - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The curr... FAILED skimage/color/tests/test_colorconv.py::test_nD_gray_conversion[shape2-rgb2gray] - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The curr... FAILED skimage/color/tests/test_colorconv.py::test_nD_gray_conversion[shape3-rgb2gray] - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The curr... FAILED skimage/color/tests/test_colorconv.py::test_nD_gray_conversion[shape4-rgb2gray] - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The curr... FAILED skimage/feature/tests/test_corner.py::test_shape_index - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is float64 w... FAILED skimage/filters/tests/test_gaussian.py::test_multichannel - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is float64... FAILED skimage/filters/tests/test_ridges.py::test_border_warning[sato] - ValueError: Unexpected warning: Convertingnp.inexactornp.floatingto a dtype is deprecated. The current result isf... FAILED skimage/filters/tests/test_ridges.py::test_border_warning[hessian] - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is... FAILED skimage/io/tests/test_pil.py::test_all_color - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is float64 which is no... FAILED skimage/io/tests/test_pil.py::test_all_mono - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is float64 which is not... FAILED skimage/restoration/tests/test_denoise.py::test_denoise_bilateral_nan - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result... FAILED skimage/segmentation/tests/test_active_contour_model.py::test_bc_deprecation - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current... FAILED skimage/segmentation/tests/test_active_contour_model.py::test_xy_coord_warning - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The curre... FAILED skimage/segmentation/tests/test_random_walker.py::test_2d_bf - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is floa... FAILED skimage/segmentation/tests/test_random_walker.py::test_2d_cg - ValueError: Unexpected warning: Convertingnp.inexactornp.floatingto a dtype is deprecated. The current result isfloa... FAILED skimage/segmentation/tests/test_random_walker.py::test_2d_cg_mg - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is f... FAILED skimage/segmentation/tests/test_random_walker.py::test_2d_cg_j - ValueError: Unexpected warning: Convertingnp.inexactornp.floatingto a dtype is deprecated. The current result isfl... FAILED skimage/segmentation/tests/test_random_walker.py::test_types - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is floa... FAILED skimage/segmentation/tests/test_random_walker.py::test_reorder_labels - ValueError: Unexpected warning: Convertingnp.inexactornp.floatingto a dtype is deprecated. The current result... FAILED skimage/segmentation/tests/test_random_walker.py::test_2d_inactive - ValueError: Unexpected warning: Convertingnp.inexactornp.floatingto a dtype is deprecated. The current result is... FAILED skimage/segmentation/tests/test_random_walker.py::test_3d - ValueError: Unexpected warning: Convertingnp.inexactornp.floatingto a dtype is deprecated. The current result isfloat64... FAILED skimage/segmentation/tests/test_random_walker.py::test_3d_inactive - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is... FAILED skimage/segmentation/tests/test_random_walker.py::test_multispectral_2d - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current resu... FAILED skimage/segmentation/tests/test_random_walker.py::test_multispectral_3d - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current resu... FAILED skimage/segmentation/tests/test_random_walker.py::test_spacing_0 - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is ... FAILED skimage/segmentation/tests/test_random_walker.py::test_spacing_1 - ValueError: Unexpected warning: Convertingnp.inexactornp.floatingto a dtype is deprecated. The current result is... FAILED skimage/segmentation/tests/test_random_walker.py::test_trivial_cases - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result ... FAILED skimage/segmentation/tests/test_random_walker.py::test_length2_spacing - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current resul... FAILED skimage/segmentation/tests/test_random_walker.py::test_isolated_seeds - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result... FAILED skimage/transform/tests/test_radon_transform.py::test_radon_circle - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is... FAILED skimage/transform/tests/test_warps.py::test_swirl - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is float64 which ... FAILED skimage/transform/tests/test_warps.py::test_downsize_anti_aliasing_invalid_stddev - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The cu... FAILED skimage/transform/tests/test_warps.py::test_boll_array_warnings - ValueError: Unexpected warning: Converting np.inexact or np.floating to a dtype is deprecated. The current result is `f... =============================================================== 35 failed, 6046 passed, 16 skipped, 18562 warnings in 264.40s (0:04:24) =============================================================== ==> FEHLER: Ein Fehler geschah in check(). Breche ab... error making: %!s(func() string=0x55f0a2e2aed0)

jdc commented on 2020-04-14 16:55 (UTC)

I'm getting an error when I try to import skimage.io.

https://hastebin.com/wukepifuxo.sql

dburkhardt commented on 2019-05-17 13:52 (UTC)

I'm getting a conflicting package error when I shouldn't be:

looking for conflicting packages...
:: python-scipy and python-scipy-openblas are in conflict. Remove python-scipy-openblas?

But python-scipy-openblas is listed as sufficient in the Dependencies table. What's going on?

Universebenzene commented on 2019-03-07 14:08 (UTC)

@bertptrs Fine, so I bring back the build() function now. Thanks!

bertptrs commented on 2019-03-07 13:58 (UTC) (edited on 2019-03-07 14:00 (UTC) by bertptrs)

You are right on the prepare() part; I've misread the diff. And while the package builds fine, the problem of compiling in package_*() is more of a semantic one. Some packages (quite a few unfortunately) compile source code in the prepare() phase, but this is incorrect. Most python packages only need to byte-compile all of their .py files. For this package it is especially noticeable as there is a lot of actual native code compilation.

The correct way to do it is: have a build() that calls python(2) setup.py build for both versions, and then in each package_ function call python(2) setup.py install …. The package function really should only be moving files from here to there. Just because you can compile the packages there doesn't mean you should. One might want to inspect the created binaries before creating a package, for example, or really just any use of makepkg --repackage.

You can see an example in the PKGBUILD for numpy: https://git.archlinux.org/svntogit/packages.git/tree/trunk/PKGBUILD?h=packages/python-numpy (and also the previous versions of this package)

Universebenzene commented on 2019-03-07 13:12 (UTC) (edited on 2019-03-07 13:13 (UTC) by Universebenzene)

Hi @bertptrs, actually I don't have build() function in the PKGBUILD, and I am modifying the source code in prepare() function , not build(). In fact for most python packages, the python setup.py install does the build at the same time, so we don't really need another build() for them. The package builds well on my PCs, so could you please tell me what kinds of errors occur on yours? Thanks for feedback.

bertptrs commented on 2019-03-07 12:45 (UTC)

Hi, I see you modified the PKGBUILD quite a bit, and with it introduced some errors. Would you mind going back to the old style?

Currently, it modifies source code in build() rather than prepare() and also compiles code in package() rather than in build(). Both are bad practices, and the PKGBUILD did this correctly before the latest commit. Please see https://wiki.archlinux.org/index.php/Python_package_guidelines

Dragonlord commented on 2019-03-05 20:24 (UTC)

Package disowned.

Universebenzene commented on 2019-02-27 12:42 (UTC) (edited on 2019-02-27 13:25 (UTC) by Universebenzene)

The PKGBUILD produced by @greyltc works well. Are you still maintaining this package? If you got any problem, we can discuss here, or please update this package ASAP. This package is related to several other packages, so if you don't update it to 0.14.2, they may all get problems.

versusvoid commented on 2019-01-29 10:02 (UTC)

Please, split PKGBUILD into two distinct packages, so I would not have to install all the python2 dependencies just to build python2 version, when I have no need for it in the first place. It would build faster, download less, there will be peace on Earth and everyone will be happy. Yeah, it would mean duplicating some common fields across two PKGBUILDs, but IMO it worth the gain.

greyltc commented on 2019-01-28 12:11 (UTC)

Fixed PKGBUILD is here: https://gist.githubusercontent.com/greyltc/757e3960127db07ed4d19c1f5c38b30f/raw/43ef5cb5abbc2c199be88eba49d1f69376431541/PKGBUILD

greyltc commented on 2019-01-27 14:32 (UTC)

Today this doesn't import because:

ImportError: cannot import name '_validate_lengths' from 'numpy.lib.arraypad' (/usr/lib/python3.7/site-packages/numpy/lib/arraypad.py)

Looks like https://github.com/scikit-image/scikit-image/issues/3586

I think a fix for this should be in the 0.14.2 release so please update asap!

andrew-wja commented on 2019-01-18 15:41 (UTC)

When I try to import the library:

ImportError: /usr/lib/python3.7/site-packages/skimage/restoration/_nl_means_denoising.cpython-37m-x86_64-linux-gnu.so: undefined symbol: fast_exp

salviati commented on 2018-10-06 15:14 (UTC)

Build fails with ==> Validating source files with sha256sums... scikit-image-0.14.1.tar.gz ... FAILED ==> ERROR: One or more files did not pass the validity check!

tocic commented on 2018-10-06 05:47 (UTC)

+1, please update

rdoursenaud commented on 2018-10-02 08:19 (UTC)

The GitHub file has been updated for v0.14.1 making the sha256sum invalid.

zhou13 commented on 2018-09-17 08:01 (UTC)

I also hope this the python3 version of this package only relies on python3 library.

Pastafarianist commented on 2018-09-16 20:34 (UTC)

Seconding @migueldvb, can only Python 3 dependencies be built for the python-scikit-image package?

tsj commented on 2018-07-20 22:59 (UTC) (edited on 2018-07-20 23:00 (UTC) by tsj)

I think python-dask needs to be a dependency. import skimage.filters complains that the dask module is missing.

python-dask depends on python-sparse which seems to have some bug, you have to disable the check step in the PKGBUILD.

davidmcinnis commented on 2017-07-28 03:56 (UTC) (edited on 2017-07-28 03:56 (UTC) by davidmcinnis)

I just added python-pyamg to the AUR, please add this to the list of optional dependencies. See: http://scikit-image.org/docs/stable/release_notes_and_installation.html#optional-requirements Thanks -Dave

b52 commented on 2017-07-21 11:45 (UTC)

As @drawm mentioned, you should add python-pywavelets as dependency!

shadeless commented on 2017-07-07 15:29 (UTC)

Did anyone successfully install all of the dependencies? I end up with this error message ImportError: The 'packaging.requirements' package is required; normally this is bundled with this package so if you get this warning, consult the packager of your distribution. I don't understand this because I have python-requirements and python2-requirements installed. Can anyone help me?

drawm commented on 2017-04-29 16:07 (UTC)

The dependency on python-pywavelets (python2-pywavelets) is missing, so there are many import errors if it has not been installed. The dependency was introduced in https://github.com/scikit-image/scikit-image/commit/c6e5c7095350e931709acd894a54b32c42375822 Please update the "depends" field in the PKGBUILD accordingly.

stick commented on 2017-04-09 18:52 (UTC)

If you want the up-to-date package, and only the version for python 3, you can modify the PKGBUILD as below. # Maintainer: Jaroslav Lichtblau <svetlemodry@archlinux.org> # Contributor: Andrzej Giniewicz <gginiu@gmail.com> #TODO (AUR optdepends): PyAMG, Astropy, SimpleITK, imread pkgbase=python-scikit-image pkgname=('python-scikit-image') pkgver=0.13.0 pkgrel=1 pkgdesc="Image processing routines for SciPy" arch=('i686' 'x86_64') url="http://scikit-image.org/" license=('BSD') makedepends=('cython' 'python-six' 'python-scipy' 'python-matplotlib' 'python-networkx' 'python-pillow') options=(!emptydirs) source=(https://pypi.python.org/packages/f0/a2/918366ba9095ed4c07646be903c795f375d978ee418136eecb0571559719/scikit-image-0.13.0.tar.gz#md5=c92b682ed77b568218423b7afe454996) sha256sums=('77a636bdc08c7668a15951894548c527f0c8c5c2abc86cb850de17551af51e3e') prepare() { cd "$srcdir" } build() { msg "Building SciKit-Image for Python3" cd "$srcdir"/scikit-image-$pkgver python setup.py build } package_python-scikit-image() { depends=('python-scipy' 'python-matplotlib' 'python-networkx' 'python-pillow') optdepends=('python-pyqt4: for imshow(x, fancy=True) and skivi' 'freeimage: for reading various types of image file formats') cd "$srcdir"/scikit-image-$pkgver python setup.py install --root="$pkgdir"/ --optimize=1 install -D LICENSE.txt "$pkgdir"/usr/share/licenses/$pkgname/LICENSE }

gypaetus commented on 2017-03-27 22:11 (UTC)

Since there is a python2-scikit-image package already, is it possible to make this PKGBUILD to build only python-scikit-image ?

daniel_shub commented on 2016-09-09 20:48 (UTC)

Would it be possible to relax the dependency on python2-pillow to simply python2-imaging? Psychopy (https://aur.archlinux.org/packages/psychopy/) is supposedly incompatible with pillow but works with PIL. The scikit documentation suggests it works with both pillow and PIL.

schmodd commented on 2016-08-26 13:49 (UTC)

I am sorry, fault seems to be on my side. Building the package the way it is described in your link works fine. Thanks for your help.

Dragonlord commented on 2016-08-21 17:44 (UTC)

Cannot reproduce the error, package builds fine on my machine with the same command. You may try building it in a clean chroot as described on https://wiki.archlinux.org/index.php/DeveloperWiki:Building_in_a_Clean_Chroot#Convenience_Way

schmodd commented on 2016-08-21 11:20 (UTC)

I get this when running "makepkg -sri": ==> Building Python2 Partial import of skimage during the build process. Traceback (most recent call last): File "setup.py", line 146, in <module> **extra File "/usr/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "setup.py", line 69, in configuration config.add_subpackage('skimage') File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage caller_level = 2) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/setup.py", line 9, in configuration config.add_subpackage('_shared') File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage caller_level = 2) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/_shared/setup.py", line 20, in configuration config.add_extension('geometry', sources=['geometry.c']) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1485, in add_extension ext = Extension(**ext_args) File "/usr/lib/python2.7/site-packages/numpy/distutils/extension.py", line 52, in __init__ export_symbols) TypeError: __init__() takes at most 4 arguments (13 given) ==> FEHLER: Ein Fehler geschah in build(). Breche ab...

soupault commented on 2016-07-22 06:09 (UTC) (edited on 2016-07-22 06:09 (UTC) by soupault)

wait, what am I even talking about... obviously we do have `dask` among the requirements: https://github.com/scikit-image/scikit-image/blob/master/requirements.txt

soupault commented on 2016-07-21 18:54 (UTC) (edited on 2016-07-22 06:10 (UTC) by soupault)

*deleted*

anntzer commented on 2016-07-21 18:46 (UTC)

Actually I would make dask a non-optional dependency; note that in its absence, trying to start e.g. `skivi` (a program in /usr/bin provided by scikit-image) raises Traceback (most recent call last): File "/usr/bin/skivi", line 5, in <module> from pkg_resources import load_entry_point File "/usr/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2928, in <module> @_call_aside File "/usr/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2914, in _call_aside f(*args, **kwargs) File "/usr/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2941, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/usr/lib/python3.5/site-packages/pkg_resources/__init__.py", line 635, in _build_master ws.require(__requires__) File "/usr/lib/python3.5/site-packages/pkg_resources/__init__.py", line 943, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/lib/python3.5/site-packages/pkg_resources/__init__.py", line 829, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'dask[array]>=0.5.0' distribution was not found and is required by scikit-image

soupault commented on 2016-05-19 19:22 (UTC)

@giniu was there any discussion? If yes, could you point me at it, please?

giniu commented on 2016-05-08 14:11 (UTC)

I think it could have stayed in community, because dask seems to be optional dependency - used only for parallel computation: https://github.com/scikit-image/scikit-image/blob/bfb6175485afc929ba2ee6f1ba73013f8fa98731/DEPENDS.txt#L30