If CellProfiler's requirements.txt file names a version of centrosome, then we should use a virtual environment to pick the version (and in the future, this strategy will make it easier to install CellProfiler when its setup becomes standardized). Do the following:
and then when running CellProfiler, source the virtual environment when running it. I'm not sure why you need to explicitly pip install pytest - setup fails for me with the stack trace below if I don't.
Traceback (most recent call last):
File "<string>", line 20, in <module>
File "/tmp/pip-r3_TYw-build/setup.py", line 111, in <module>
version="1.0.2",
File "/imaging/analysis/CPCluster/CellProfiler-2.0/builds/redhat_6/lib/python2.7/distutils/core.py", line 112, in setup
_setup_distribution = dist = klass(attrs)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/dist.py", line 268, in __init__
self.fetch_build_eggs(attrs['setup_requires'])
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/dist.py", line 313, in fetch_build_eggs
replace_conflicting=True,
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/pkg_resources/__init__.py", line 830, in resolve
dist = best[req.key] = env.best_match(req, ws, installer)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1075, in best_match
return self.obtain(req, installer)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1087, in obtain
return installer(requirement)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/dist.py", line 380, in fetch_build_egg
return cmd.easy_install(req)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 629, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 659, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 842, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1070, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1056, in run_setup
run_setup(setup_script, args)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 240, in run_setup
raise
File "/imaging/analysis/CPCluster/CellProfiler-2.0/builds/redhat_6/lib/python2.7/contextlib.py", line 35, in __exit__
self.gen.throw(type, value, traceback)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 193, in setup_context
yield
File "/imaging/analysis/CPCluster/CellProfiler-2.0/builds/redhat_6/lib/python2.7/contextlib.py", line 35, in __exit__
self.gen.throw(type, value, traceback)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 152, in save_modules
yield saved
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 126, in __exit__
self._saved = UnpickleableException.dump(type, exc)
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
File "/imaging/cold/People/Lee/venv/cpvenvtest/lib/python2.7/site-packages/setuptools/sandbox.py", line 110, in dump
return cls.dump(cls, cls(repr(exc)))
MemoryError
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-r3_TYw-build
If CellProfiler's requirements.txt file names a version of centrosome, then we should use a virtual environment to pick the version (and in the future, this strategy will make it easier to install CellProfiler when its setup becomes standardized). Do the following:
and then when running CellProfiler, source the virtual environment when running it. I'm not sure why you need to explicitly
pip install pytest- setup fails for me with the stack trace below if I don't.