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I'm stumped. I'm developing some enhancements to scikit-image which are failing the automated build tests, probably due to rounding errors. I therefore need to get the automated tests running on my Windows system so that I can debug and work out what's wrong. I've so far tried two approaches, neither of which are working:

  1. In my Anaconda Python 3.6 environment, when I try to run the automated tests, I am getting the following error:

    RuntimeError: module compiled against API version 0xc but this version of numpy is 0xb

    ...which I have found reference to in other contexts, but have not been able to eliminate.

  2. Since the automated test do run (but fail) on a Python 3.5-based system, I thought things might work if I tried a local Python 3.5 environment. Here, I am running into the issue that, despite being installed, the environment cannot find the MS C++ compiler cl.exe. It is installed in C:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\VC\Tools\MSVC\14.15.26726\bin\HostX86\x64\ and is found and executed by my Python 3.6 environment, but my Python 3.5 environment doesn't find it despite me adding that directory to my PATH. I should add that my Python 3.6 environment finds it without the directory being added to the PATH. I understand that both Python 3.5 and 3.6 use MSVC 14.0.

I would prefer to fix the problem in my Python 3.6 environment if possible. Any assistance much appreciated.

Update

I have made a box-fresh Python 3.6 conda environment as follows:

conda create --name sk36 python=3.6 conda activate sk36 conda install scikit-image --only-deps conda install cython git clone https://github.com/scikit-image/scikit-image.git cd scikit-image pip install -e . pytest skimage/feature

The specific error I am getting is as follows:

..\Anaconda3\lib\site-packages\py\_path\local.py:662: in pyimport __import__(modname) skimage\__init__.py:135: in <module> from .data import data_dir skimage\data\__init__.py:13: in <module> from ..io import imread, use_plugin skimage\io\__init__.py:7: in <module> from .manage_plugins import * skimage\io\manage_plugins.py:24: in <module> from .collection import imread_collection_wrapper skimage\io\collection.py:12: in <module> from ..external.tifffile import TiffFile skimage\external\tifffile\__init__.py:1: in <module> from .tifffile import imsave, imread, imshow, TiffFile, TiffWriter, TiffSequence skimage\external\tifffile\tifffile.py:292: in <module> from . import _tifffile E RuntimeError: module compiled against API version 0xc but this version of numpy is 0xb

...which appears to have something to do with tifffile. Since this package wasn't originally explicitly installed in my new environment, I tried installing various versions of it, including some which downgraded numpy and scipy. Still the same error as above.

Having done some more research it would appear that something is seeing numpy 1.13.x when in fact version 1.15.4 is installed. Here is the full output from conda list:

# Name Version Build Channel blas 1.0 mkl anaconda ca-certificates 2018.03.07 0 anaconda certifi 2018.10.15 py36_0 anaconda cloudpickle 0.6.1 py36_0 anaconda cycler 0.10.0 py36h009560c_0 anaconda cython 0.29 py36ha925a31_0 anaconda dask-core 0.20.0 py36_0 anaconda decorator 4.3.0 py36_0 anaconda freetype 2.9.1 ha9979f8_1 anaconda icc_rt 2017.0.4 h97af966_0 anaconda icu 58.2 ha66f8fd_1 anaconda imageio 2.4.1 py36_0 anaconda intel-openmp 2019.0 118 anaconda jpeg 9b hb83a4c4_2 anaconda kiwisolver 1.0.1 py36h6538335_0 anaconda libpng 1.6.35 h2a8f88b_0 anaconda libtiff 4.0.9 h36446d0_2 anaconda matplotlib 3.0.1 py36hc8f65d3_0 anaconda mkl 2019.0 118 anaconda mkl_fft 1.0.6 py36hdbbee80_0 anaconda mkl_random 1.0.1 py36h77b88f5_1 anaconda networkx 2.2 py36_1 anaconda numpy 1.15.4 py36ha559c80_0 anaconda numpy-base 1.15.4 py36h8128ebf_0 anaconda olefile 0.46 py36_0 anaconda openssl 1.0.2p hfa6e2cd_0 anaconda package_has_been_revoked 1.0 0 enable_revoked pillow 5.3.0 py36hdc69c19_0 anaconda pip 18.1 py36_0 anaconda pyparsing 2.3.0 py36_0 anaconda pyqt 5.9.2 py36h6538335_2 anaconda python 3.6.7 h33f27b4_1 anaconda python-dateutil 2.7.5 py36_0 anaconda pytz 2018.7 py36_0 anaconda pywavelets 1.0.1 py36h8c2d366_0 anaconda qt 5.9.6 vc14h1e9a669_2 anaconda scikit-image 0.15.dev0 <pip> scipy 1.1.0 py36h4f6bf74_1 anaconda setuptools 40.5.0 py36_0 anaconda sip 4.19.8 py36h6538335_0 anaconda six 1.11.0 py36_1 anaconda sqlite 3.25.2 hfa6e2cd_0 anaconda tifffile 0.15.1 py36h452e1ab_1001 conda-forge tk 8.6.8 hfa6e2cd_0 anaconda toolz 0.9.0 py36_0 anaconda tornado 5.1.1 py36hfa6e2cd_0 anaconda vc 14.1 h21ff451_3 anaconda vs2015_runtime 15.5.2 3 anaconda wheel 0.32.2 py36_0 anaconda wincertstore 0.2 py36h7fe50ca_0 anaconda zlib 1.2.11 h8395fce_2 anaconda

Update 2

I've solved the problem for Python 3.6, and I think there's enough information above for the astute to be able to work out what was wrong. I'll put the solution in an answer below.

A cleanly built Python 3.5 environment can't find the compiler, so that issue still remains.

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  • I've personally never been successful with compiling numpy or scipy from source on windows. I've always just gone with the anaconda distribution's precompiled installer. Commented Nov 9, 2018 at 16:33
  • @Aaron - I'm not trying to compile either of those packages. Commented Nov 9, 2018 at 16:56
  • They're all part of the scipy.org ecosystem, so they're quite related. I haven't personally tried to compile scikit-image, but I'm sure much of the codebase is similar... Commented Nov 9, 2018 at 17:16
  • Also the error itself sounds like it is in fact numpy that needs re-compiling against a newer base... Commented Nov 9, 2018 at 17:18
  • Thanks. Which API is being referred to? Commented Nov 9, 2018 at 17:54

2 Answers 2

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One approach you could try is to upgrade your numpy with

pip install numpy --upgrade

as described here: RuntimeError: module compiled against API version a but this version of numpy is 9

Otherwise (if for some reason you cannot upgrade numpy) I would suggest going with a virtual environment for scikit-image project. I just tried it on Windows 10 and was able to successfully execute tests. My steps (from cmd, inside the project folder):

  • conda uninstall scikit-image to remove any previously built/installed versions
  • conda -n scikit-image python=3.6 to create a virtual environment for this project (I used python 3.6, but you can change it to 3.5)
  • activate scikit-image activated the new virtual env
  • pip install -r requirements.txt -- installed dependencies (without this step I wasn't getting the dependencies for tests installed)
  • pip install -e .
  • pytest
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Thanks for your input. I have tried something very similar, using box fresh 3.5 and 3.6 conda environments. The 3.5 environment can't find the compiler, and the 3.6 one raises the numpy API error when running pytest.
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It turns out that pytest wasn't actually installed in the correct environment, it was being invoked from base which did indeed have numpy 1.13.3 installed. Installing it in the cleanly built Python 3.6 environment solved the problem for Python 3.6 at least.

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