Pip install error from official 1.1.0 tarball about microbecensus

[boulund]

Nevermind, I commented out the section in setup.py that tries to mess with the file permissions, now it appears to work just fine. At least I have an executable Python script in my path called run_microbe_census.py and it produces nice help output. I'll report back when I've tried running it for real later this week. I'll leave this here if someone else encounters the same issue.

For reference, I commented out the following lines in setup.py:

MicrobeCensus/setup.py

Lines 6 to 14 in d91b465

	class my_install_lib(install_lib.install_lib):
	""" Make all packaged binaries executable """
	def run(self):
	install_lib.install_lib.run(self)
	for fn in self.get_outputs():
	if fn.split('/')[-2] == 'bin':
	mode = ((os.stat(fn).st_mode) | 0555) & 07777
	log.info("changing mode of %s to %o", fn, mode)
	os.chmod(fn, mode)

[boulund]

Deleted everything again this morning and started over. Turns out I managed to fail to install pip in the new conda environment I created, so it tried installing MicrobeCensus in the root conda environment without me realizing. I started over and created a new conda environment properly and installed MicrobeCensus according to instructions, and all worked just fine. Sorry for creating an unnecessary issue :)

[snayfach]

No worries! Glad you got things working. Just FYI, the github release is a newer version than is present on pip.

[boulund]

Yes, I noticed that the github version is newer. Newer is always better, right? :).
It seems to be working just fine for me now. No issues at all (so far)!