Thus I expected naively that pip install . and python setup.py install should have the same results.

they process install_requires with different code, so things could turn out differently.

I have a reproducible case when the dependency handling differs if you use pip install -r requirements.txt or when you use python setup.py install
https://github.com/zeromq/pyzmq/issues/414#issuecomment-24679800

I looked at this case, but atleast for me, the results were the same in all 3 cases

(note that this project splits requirements.txt to generate 'install_requires')

1) python setup.py install

2) pip install .

3) pip install -r requirements.txt

from "pip list" after the installs:

anyjson (0.3.3)

configparser (3.3.0r2)

coverage (3.6)

docutils (0.11)

Jinja2 (2.7.1)

MarkupSafe (0.18)

picomongo (0.6)

Pygments (1.6)

pymongo (2.6.2)

pyzmq (13.1.0)

satlive (0.8.0)

Sphinx (1.2b2)

btw, pip<1.4 has a bug where a stale build directory can lead to unexpected results.

check for the offending project in <venv>/build (if using a virtualenv), or if using a global python /tmp/pip-build-<username>