CI failing on OSX

[jeromekelleher]

Travis builds on OSX are failing with some problem due to certifi, e.g. (https://travis-ci.org/tskit-dev/tskit/jobs/588432325)

uilding wheels for collected packages: sphinx-argparse, PyVCF, snowballstemmer, inflection
679  Building wheel for sphinx-argparse (setup.py) ... done
680  Created wheel for sphinx-argparse: filename=sphinx_argparse-0.2.5-cp36-none-any.whl size=11552 sha256=7254d149ea26c0c4dfdf71238858090c055d7c32b70717c6246e935b583cd0ea
681  Stored in directory: /Users/travis/Library/Caches/pip/wheels/2a/18/1b/4990a1859da4edc77ab312bc2986c08d2733fb5713d06e44f5
682  Building wheel for PyVCF (setup.py) ... done
683  Created wheel for PyVCF: filename=PyVCF-0.6.8-cp36-none-any.whl size=36008 sha256=b6936f71c9482ed2eff7ea49266c4653ff652afef2844c5c63a8d93dbc54bfd7
684  Stored in directory: /Users/travis/Library/Caches/pip/wheels/81/91/41/3272543c0b9c61da9c525f24ee35bae6fe8f60d4858c66805d
685  Building wheel for snowballstemmer (setup.py) ... done
686  Created wheel for snowballstemmer: filename=snowballstemmer-1.9.1-cp36-none-any.whl size=101576 sha256=b730b6d73c3c17ec8721b4c185140c68aa1993362a423186ffef6fb059cd11e3
687  Stored in directory: /Users/travis/Library/Caches/pip/wheels/ae/9b/66/6b8f275ec6dfa2138a56faaf2b4314ca44a4746286560d5578
688  Building wheel for inflection (setup.py) ... done
689  Created wheel for inflection: filename=inflection-0.3.1-cp36-none-any.whl size=6076 sha256=c2174d7df15d6fa06d0a14cec718e552c6ad2af91acfb1335ab6378d6fe1b74c
690  Stored in directory: /Users/travis/Library/Caches/pip/wheels/9f/5a/d3/6fc3bf6516d2a3eb7e18f9f28b472110b59325f3f258fe9211
691Successfully built sphinx-argparse PyVCF snowballstemmer inflection
692Installing collected packages: coverage, chardet, urllib3, idna, certifi, requests, codecov, pyflakes, mccabe, pycodestyle, entrypoints, flake8, newick, sphinxcontrib-htmlhelp, pytz, babel, snowballstemmer, sphinxcontrib-jsmath, Pygments, sphinxcontrib-applehelp, sphinxcontrib-qthelp, sphinxcontrib-devhelp, imagesize, docutils, packaging, sphinxcontrib-serializinghtml, MarkupSafe, Jinja2, alabaster, sphinx, sphinx-argparse, sphinx-rtd-theme, sphinx-issues, breathe, PyVCF, inflection, Markdown, python-jsonschema-objects
693  Found existing installation: certifi 2016.9.26
694ERROR: Cannot uninstall 'certifi'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
695The command "pip install -r python/requirements/development.txt" failed and exited with 1 during .

[hyanwong]

Perhaps using pip install --ignore-installed would help here? stacks-network/stacks-core#504

[jeromekelleher]

Do you want to try it out? I don't have time to sort this out I'm afraid.

[hyanwong]

Happy to try

[hyanwong]

Adding - pip install --ignore-installed certifi seems a bit hacky, but as it's only in the travis file, I guess that's OK.

I also cherry-picked this onto #320 to check it really did allow this to work now (it does). Up to you if you want to merge this PR first, in which case I can rebase #320, or simply merge #320 and forget about this PR.

[jeromekelleher]

Good stuff @hyanwong, perfect solution to scrappy problem.