pip install -e fails with compile error

[ctb]

The command:

pip install -e git+https://github.com/ged-lab/khmer.git@master#egg=khmer

fails with:

khmer/_khmermodule.cc:17:20: fatal error: khmer.hh: No such file or directory

on ami-c17ec8a8, which admittedly is an old Ubuntu install. I did upgrade pip to the latest version first, however.

[mr-c]

On Sat, Mar 29, 2014 at 11:09 AM, C. Titus Brown
notifications@github.comwrote:

pip install -e git+https://github.com/ged-lab/khmer.git@master#egg=khmer

Confirmed on Ubuntu 12.04.4 LTS

This is a Setuptools / distutils issue with how they handle command options
of dependent commands. That pip command calls setup.py develop which
executes the build_ext command. When setup.py build_ext is called the
options specified in setup.cfg "[build_ext]" stanza are correctly
incorporated; this is not the case when the build_ext command is executed
by the develop command. I ran into this with the nosetests command recently.

This appears to be due to the fact that we extend the setuptools
'build_ext' to ensure that zlib & bzip's are configured & compiled. When I
disable the override all goes correctly.

I can work around this by moving the include directories back into setup.py
from setup.cfg. A better fix would clean up several issues I've been
experiencing.

[mr-c]

1. Subclassing the distutils version of build_ext instead of the setuptools version doesn't solve the problem

2. It appears that the subclassing is the problem. Even an empty subclass (which should silently pass through to distutils or setuptools) gives the same symptoms.

[mr-c]

#353 now includes a monkeypatch to fix the real problem
The Distribution.reinitialize_command() method implies that you get the same command that Distribution.get_command_obj() give you but fails to set options that were supplied in config files or on the command line like get_command_obj() does.

[ctb]

On Sat, Mar 29, 2014 at 12:14:54PM -0700, Michael R. Crusoe wrote:

#353 now includes a monkeypatch to fix the real problem
The Distribution.reinitialize_command() method implies that you get the same command that Distribution.get_command_obj() give you but fails to set options that were supplied in config files or on the command line like get_command_obj() does.

Should we file this as a bug report in Python?

C. Titus Brown, ctb@msu.edu

[mr-c]

@ctb Yes. Likely it won't be fixed there (as it does change behavior); setuptools would be a good place to include the monkeypatch.

[mr-c]

pip install -e git+https://github.com/ged-lab/khmer.git@fix/build_ext-cfg-workaround#egg=khmer works for me