Pip install broken about staintools HOT 7 CLOSED

Thanks @fortunechen. Yes I also used to use the conda distribution of spams. More recently spams was made available on PyPI so I wanted to switch to that to make install simpler (not everyone uses conda). However it seems to be too buggy at the moment so I will consider to revert to conda again.

from staintools.

After commenting out the following lines,

# with open('README.md') as f:
#     readme = f.read()

setup(
    name='staintools',
    version='2.1.1',
    description='A package for tissue image stain normalization, augmentation and more.',
#     long_description=readme,
    author='Peter Byfield',
    author_email='[email protected]',
    url='https://github.com/Peter554/StainTools',
    packages=find_packages(exclude=('tests')),
    install_requires=[
        'numpy',
        'opencv-python',
        'spams',
        'matplotlib'
    ]
)

I tried installing from a local cloned directory using pip install -e . and triggered the following error:

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ffbvu0zn/spams/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-3qf2_y4e/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-ffbvu0zn/spams/

from staintools.

I haven't seen the first error before regarding readme encoding, just it should be easily fixable.

I'm more concerned about the second one regarding SPAMS. This is a package dependency that gives rather a headache it seems. It was recently made available of PyPI but unfortunately the install pip install spams seems very buggy. Ideally that would be fixed or we would get rid of this dependency some how (but so far I haven't found anything suitable - sklearn did seem to have something similar but it was much slower).

from staintools.

I've sent the SPAMS dev team an email to ask about their pip install.

from staintools.

After commenting out the following lines,

# with open('README.md') as f:
#     readme = f.read()

setup(
    name='staintools',
    version='2.1.1',
    description='A package for tissue image stain normalization, augmentation and more.',
#     long_description=readme,
    author='Peter Byfield',
    author_email='[email protected]',
    url='https://github.com/Peter554/StainTools',
    packages=find_packages(exclude=('tests')),
    install_requires=[
        'numpy',
        'opencv-python',
        'spams',
        'matplotlib'
    ]
)

I tried installing from a local cloned directory using pip install -e . and triggered the following error:

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ffbvu0zn/spams/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-3qf2_y4e/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-ffbvu0zn/spams/

I installed spams first by using conda https://anaconda.org/conda-forge/python-spams, and commented install_requires lines, then pip install -e . worked.

from staintools.

Response from SPAMS says they are looking into it but don't expect anything too soon. So for now I'll keep this issue open and have updated the README to advise using conda if possible.

pip install is currently broken due to the dependency on SPAMS. This issue has been raised with the SPAMS developers. In the meantime if you use conda you may have better luck resolving the SPAMS dependency via conda-forge:

https://anaconda.org/conda-forge/python-spams

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Update:

• long_description=readme issue should now be resolved.
• SPAMS install. For now have removed from setup.py and updated README to guide users to the conda option.

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