Pytest error due to Build Fail

tamimfatahi · September 8, 2024, 5:45pm

After following the developer instructions here, I’ve had trouble getting pytest to work properly. Here is the error:

============================================================== 2 failed, 8661 passed, 28 skipped, 89 xfailed in 452.14s (0:07:32) ================================================================
(skimage-dev) abdullahfatahi@98CJG5J-18B-S scikit-image % pytest skimage
ImportError while loading conftest '/Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/conftest.py'.
skimage/__init__.py:128: in <module>
    _raise_build_error(e)
skimage/__init__.py:103: in _raise_build_error
    raise ImportError(
E   ImportError: cannot import name 'geometry' from 'skimage._shared' (/Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_shared/__init__.py)
E   It seems that scikit-image has not been built correctly.
E
E   Your install of scikit-image appears to be broken.
E   Try re-installing the package following the instructions at:
E   https://scikit-image.org/docs/stable/user_guide/install.html

Everything seems to have built fine as well (shortened log due to character limit):

(skimage-dev) abdullahfatahi@98CJG5J-18B-S scikit-image % spin build -v
$ meson setup build --prefix=/usr
The Meson build system
Version: 1.5.1
Source dir: /Users/abdullahfatahi/PycharmProjects/scikit-image
Build dir: /Users/abdullahfatahi/PycharmProjects/scikit-image/build
Build type: native build
Project name: scikit-image
Project version: 0.24.1rc0.dev0
C compiler for the host machine: cc (clang 14.0.3 "Apple clang version 14.0.3 (clang-1403.0.22.14.1)")
C linker for the host machine: cc ld64 857.1
C++ compiler for the host machine: c++ (clang 14.0.3 "Apple clang version 14.0.3 (clang-1403.0.22.14.1)")
C++ linker for the host machine: c++ ld64 857.1
Cython compiler for the host machine: cython (cython 3.0.11)
Host machine cpu family: x86_64
Host machine cpu: x86_64
Compiler for C supports arguments -Wno-unused-function: YES 
Library m found: YES
Checking if "-Wl,--version-script" : links: NO 
Program cython found: YES (/Users/abdullahfatahi/envs/skimage-dev/bin/cython)
Program pythran found: YES (/Users/abdullahfatahi/envs/skimage-dev/bin/pythran)
Program cp found: YES (/bin/cp)
Program python3 found: YES (/Users/abdullahfatahi/envs/skimage-dev/bin/python)
Did not find pkg-config by name 'pkg-config'
Found pkg-config: NO
Run-time dependency python found: YES 3.10
Program _build_utils/cythoner.py found: YES (/Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py)
Compiler for C++ supports arguments -Wno-cpp: YES 
Build targets in project: 59

scikit-image 0.24.1rc0.dev0

  User defined options
    prefix: /usr

Found ninja-1.11.1.git.kitware.jobserver-1 at /Users/abdullahfatahi/envs/skimage-dev/bin/ninja
$ meson compile -v -C build
INFO: autodetecting backend as ninja
INFO: calculating backend command to run: /Users/abdullahfatahi/envs/skimage-dev/bin/ninja -C /Users/abdullahfatahi/PycharmProjects/scikit-image/build -v
ninja: Entering directory `/Users/abdullahfatahi/PycharmProjects/scikit-image/build'
[1/171] /Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py ../skimage/_shared/fast_exp.pyx skimage/_shared/fast_exp.cpython-310-darwin.so.p/fast_exp.c
[2/171] /Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py ../skimage/feature/censure_cy.pyx skimage/feature/censure_cy.cpython-310-darwin.so.p/censure_cy.c
[3/171] /Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py ../skimage/draw/_draw.pyx skimage/draw/_draw.cpython-310-darwin.so.p/_draw.c
[4/171] /Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py ../skimage/_shared/geometry.pyx skimage/_shared/geometry.cpython-310-darwin.so.p/geometry.c
[5/171] /Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py ../skimage/_shared/transform.pyx skimage/_shared/transform.cpython-310-darwin.so.p/transform.c
[6/171] /Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py ../skimage/feature/_hoghistogram.pyx skimage/feature/_hoghistogram.cpython-310-darwin.so.p/_hoghistogram.c
[7/171] /Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py ../skimage/feature/_canny_cy.pyx skimage/feature/_canny_cy.cpython-310-darwin.so.p/_canny_cy.c
[8/171] /Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py ../skimage/feature/_sift.pyx skimage/feature/_sift.cpython-310-darwin.so.p/_sift.c
[9/171] /Users/abdullahfatahi/PycharmProjects/scikit-image/skimage/_build_utils/cythoner.py ../skimage/feature/corner_cy.pyx skimage/feature/corner_cy.cpython-310-darwin.so.p/corner_cy.c
.
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$ meson install --only-changed -C build --destdir ../build-install
ninja: Entering directory `/Users/abdullahfatahi/PycharmProjects/scikit-image/build'
ninja: no work to do.
Installing skimage/_shared/transform.cpython-310-darwin.so to /Users/abdullahfatahi/PycharmProjects/scikit-image/build/../build-install/usr/lib/python3.10/site-packages/skimage/_shared
Installing skimage/_shared/fast_exp.cpython-310-darwin.so to /Users/abdullahfatahi/PycharmProjects/scikit-image/build/../build-install/usr/lib/python3.10/site-packages/skimage/_shared
Installing skimage/_shared/geometry.cpython-310-darwin.so to /Users/abdullahfatahi/PycharmProjects/scikit-image/build/../build-install/usr/lib/python3.10/site-packages/skimage/_shared
Installing skimage/_shared/interpolation.cpython-310-darwin.so to /Users/abdullahfatahi/PycharmProjects/scikit-image/build/../build-install/usr/lib/python3.10/site-packages/skimage/_shared
Installing skimage/draw/_draw.cpython-310-darwin.so to /Users/abdullahfatahi/PycharmProjects/scikit-image/build/../build-install/usr/lib/python3.10/site-packages/skimage/draw
.
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Running custom install script '/Users/abdullahfatahi/envs/skimage-dev/bin/python /Users/abdullahfatahi/PycharmProjects/scikit-image/build/meson-private/pycompile.py python-3.10-installed.json 0'
Compiling '/Users/abdullahfatahi/PycharmProjects/scikit-image/build/../build-install/usr/lib/python3.10/site-packages/skimage/__init__.py'...
Compiling '/Users/abdullahfatahi/PycharmProjects/scikit-image/build/../build-install/usr/lib/python3.10/site-packages/skimage/conftest.py'...
Compiling '/Users/abdullahfatahi/PycharmProjects/scikit-image/build/../build-install/usr/lib/python3.10/site-packages/skimage/_shared/__init__.py'...
Compiling '/Users/abdullahfatahi/PycharmProjects/scikit-image/build/../build-install/usr/lib/python3.10/site-packages/skimage/_shared/_dependency_checks.py'...
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I’ve redone the procedure to no luck. Apologies if this is an easy fix as I am fairly new to this. Thanks!

lagru · September 12, 2024, 4:05pm

No worries @tamimfatahi. There are sometimes still some hiccups with the new meson based approach and I’ve seen pytest fail on meson-compiled setups before. Could you try running these command to see if they pass?

spin build --clean
spin test  # Should be more robust than pytest
spin test -- skimage/  # Alternative

lagru · September 12, 2024, 4:08pm

Also note, that our most recent (working) version is usually on our “dev” version of the docs (see the version switcher on the top right of the docs).

stefanv · September 12, 2024, 6:09pm

You definitely cannot run pytest in the skimage source directory like that. If you build with meson, it installs into build-install, and that needs to be added to path.

Editable install makes that a bit easier, so you could do pip install --no-isolation -e ., and then run pytest, and that should be fine.

But, spin is our recommended avenue of doing these things, so I concurn with Lars’s recommendation.

Let us know if that works!

tamimfatahi · September 20, 2024, 6:50pm

Thank you both! I did a clean install and followed the dev version instead, now everything seems to be working properly.