Installing via `setup.py develop` fails - pip works

Question

My python package footools needs html5lib via install_requires in setup.py.

setup.py develop fails

Installing via setup.py develop fails:

cd src/footools/
python setup.py develop

Processing dependencies for footools==2016.205
Searching for html5lib==0.9999999
Reading https://source.example.com/pypi/simple/html5lib/
Download error on https://source.example.com/pypi/simple/html5lib/: 
   [Errno 185090050] _ssl.c:354: error:0B084002:x509 
   certificate routines:X509_load_cert_crl_file:system lib -- 
   Some packages may not be found!
Couldn't find index page for 'html5lib' (maybe misspelled?)

pip works

But direct download works:

bar@workdevel123:~/src/footools> pip install html5lib==0.9999999
/home/bar/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:79: 
InsecurePlatformWarning: A true SSLContext object is not available. 
This prevents urllib3 from configuring SSL appropriately
and may cause certain SSL connections to fail. 
For more information, see 
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
Collecting html5lib==0.9999999
/home/bar/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:79: 
    InsecurePlatformWarning: A true SSLContext object is not available. 
    This prevents urllib3 from configuring SSL appropriately and
    may cause certain SSL connections to fail. 
    For more information,
    see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
  Downloading https://source.example.com/pypi/packages/html5lib-0.9999999.tar.gz
Requirement already satisfied (use --upgrade to upgrade):
six in /usr/lib/python2.7/site-packages (from html5lib==0.9999999)
Installing collected packages: html5lib
  Running setup.py install for html5lib
Successfully installed html5lib-0.9999999

Questions

What is the difference between these two methods?

Why are they different?

What is the correct way to install a dependency in python?

setup.py

The setup.py is not special:

import setuptools

setuptools.setup(
    name='foo',
    version='2016.210',
    long_description=open('README.txt').read(),
    packages=setuptools.find_packages(),
    install_requires=[
        # about twenty packages before this line
        'html5lib==0.9999999'
],
    include_package_data=True,
    entry_points={
        'console_scripts': [
            'foo=foo.utils.bar:main',
        ],
    },
)

Answer 1

python setup.py develop, or setuptools in general uses easy_install to satisfy dependencies which in turn uses urllib2 whereas pip uses requests. See here for easy_install vs pip.
pip is more modern and among other things has capability to uninstall packages and complies with PEP 438 -- Transitioning to release-file hosting on PyPI. You can achieve the same thing as python setup.py develop with pip install -e src/footools/, note if the project path is in the current directory use, ./footools.

The requests package bundles CA certs in the package itself, python -c 'import pip;print(pip.download.requests.certs.where())'.

setuptools uses system installed CA certs python -c 'from setuptools import ssl_support;print(ssl_support.cert_paths)'.

You have to update system installed CA certs using tools like update-ca-certificates for Ubuntu to either update CA certs automatically or download from https://curl.haxx.se/docs/caextract.html and install into one of the paths shown by setuptools or set setuptools.ssl_support.cert_paths to an empty sequence like [] and do pip install certifi.
Calling setuptools.ssl_support.find_ca_bundle() will reveal the location of CA certs.