Cannot import segmentify (or run example script) if installed from PyPI

[GenevieveBuckley]

Cannot import segmentify after installation from PyPI following the instructions in the README, but works fine from local installation. Is it just me that has this issue, or does the PyPI release need updating?

My first thought was that the release on PyPI was just an empty placeholder, but this PR suggests that it should be functional (#22). I have a conda environment with all the correct dependencies already installed. When I install segmentify from PyPI, I can't import segmentify (which means the example script doesn't run). When I uninstall the PyPI version and install segmentify locally from the master branch, the example script launches fine.

Details:

(segmentify) genevieve@MU00060583:~/Documents$ pip install segmentify
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
Processing /home/genevieve/.cache/pip/wheels/d8/a2/f4/ae0b5c77b1fe14e6a20b882550eed4d503182b5ac17e474df9/segmentify-0.0.1-py3-none-any.whl
Installing collected packages: segmentify
Successfully installed segmentify-0.0.1
(segmentify) genevieve@MU00060583:~/Documents$ conda list
# packages in environment at /home/genevieve/anaconda3/envs/segmentify:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
alabaster                 0.7.12                   pypi_0    pypi
babel                     2.8.0                    pypi_0    pypi
backcall                  0.1.0                    pypi_0    pypi
ca-certificates           2019.11.27                    0  
certifi                   2019.11.28               py37_0  
chardet                   3.0.4                    pypi_0    pypi
cycler                    0.10.0                   pypi_0    pypi
dask                      2.9.2                    pypi_0    pypi
decorator                 4.4.1                    pypi_0    pypi
docutils                  0.16                     pypi_0    pypi
freetype-py               2.1.0.post1              pypi_0    pypi
fsspec                    0.6.2                    pypi_0    pypi
idna                      2.8                      pypi_0    pypi
imageio                   2.6.1                    pypi_0    pypi
imagesize                 1.2.0                    pypi_0    pypi
ipykernel                 5.1.4                    pypi_0    pypi
ipython                   7.11.1                   pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
jedi                      0.16.0                   pypi_0    pypi
jinja2                    2.11.0                   pypi_0    pypi
joblib                    0.14.1                   pypi_0    pypi
jupyter-client            5.3.4                    pypi_0    pypi
jupyter-core              4.6.1                    pypi_0    pypi
kiwisolver                1.1.0                    pypi_0    pypi
ld_impl_linux-64          2.33.1               h53a641e_7  
libedit                   3.1.20181209         hc058e9b_0  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 9.1.0                hdf63c60_0  
libstdcxx-ng              9.1.0                hdf63c60_0  
llvmlite                  0.31.0                   pypi_0    pypi
markupsafe                1.1.1                    pypi_0    pypi
matplotlib                3.1.2                    pypi_0    pypi
napari                    0.2.10                   pypi_0    pypi
ncurses                   6.1                  he6710b0_1  
networkx                  2.4                      pypi_0    pypi
numba                     0.47.0                   pypi_0    pypi
numpy                     1.18.1                   pypi_0    pypi
numpydoc                  0.9.2                    pypi_0    pypi
openssl                   1.1.1d               h7b6447c_3  
packaging                 20.1                     pypi_0    pypi
parso                     0.6.0                    pypi_0    pypi
pexpect                   4.8.0                    pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pillow                    7.0.0                    pypi_0    pypi
pip                       20.0.2                   py37_0  
prompt-toolkit            3.0.3                    pypi_0    pypi
ptyprocess                0.6.0                    pypi_0    pypi
pygments                  2.5.2                    pypi_0    pypi
pyopengl                  3.1.5                    pypi_0    pypi
pyparsing                 2.4.6                    pypi_0    pypi
pyside2                   5.14.0                   pypi_0    pypi
python                    3.7.6                h0371630_2  
python-dateutil           2.8.1                    pypi_0    pypi
pytz                      2019.3                   pypi_0    pypi
pywavelets                1.1.1                    pypi_0    pypi
pyzmq                     18.1.1                   pypi_0    pypi
qtconsole                 4.6.0                    pypi_0    pypi
qtpy                      1.9.0                    pypi_0    pypi
readline                  7.0                  h7b6447c_5  
requests                  2.22.0                   pypi_0    pypi
scikit-image              0.16.2                   pypi_0    pypi
scikit-learn              0.22.1                   pypi_0    pypi
segmentify                0.0.1                    pypi_0    pypi
setuptools                45.1.0                   py37_0  
shiboken2                 5.14.0                   pypi_0    pypi
six                       1.14.0                   pypi_0    pypi
snowballstemmer           2.0.0                    pypi_0    pypi
sphinx                    2.3.1                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.1                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.1                    pypi_0    pypi
sphinxcontrib-htmlhelp    1.0.2                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      1.0.2                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.3                    pypi_0    pypi
sqlite                    3.30.1               h7b6447c_0  
tk                        8.6.8                hbc83047_0  
toolz                     0.10.0                   pypi_0    pypi
torch                     1.4.0                    pypi_0    pypi
torchvision               0.5.0                    pypi_0    pypi
tornado                   6.0.3                    pypi_0    pypi
traitlets                 4.3.3                    pypi_0    pypi
urllib3                   1.25.8                   pypi_0    pypi
vispy                     0.6.4                    pypi_0    pypi
wcwidth                   0.1.8                    pypi_0    pypi
wheel                     0.33.6                   py37_0  
wrapt                     1.11.2                   pypi_0    pypi
xz                        5.2.4                h14c3975_4  
zlib                      1.2.11               h7b6447c_3  
(segmentify) genevieve@MU00060583:~/Documents$ python
Python 3.7.6 (default, Jan  8 2020, 19:59:22) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import segmentify
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'segmentify'
>>> 

Tthen if I uninstall the PyPI version of segmentify and install it locally from the master branch:

pip uninstall segmentify
git clone [email protected]:transformify-plugins/segmentify.git
cd segmentify
pip install .

...things work fine.

[sofroniewn]

I can try and get a functional version up on pypi, thanks for fixing #19 - that will help