Clipper plugin not pulling dependency from PyPI

[Tristan Croll]

Linux builds of the core of Clipper-Python are now on PyPI (at ​https://pypi.org/project/clipper-python/#files) and some time back I rewrote the ChimeraX Clipper plugin to rely on that. This *was* working fine, but when I downloaded the latest ChimeraX build and ran make app-install in the Clipper directory, I got the below:

{{{Executing: devel install .
running build
running build_py
running test
Searching for Clipper-Python>=0.1
Reading ​https://pypi.python.org/simple/Clipper-Python/
No local packages or working download links found for Clipper-Python>=0.1
Traceback (most recent call last):

File "/home/tic20/apps/chimerax/lib/python3.6/distutils/core.py", line 148, in setup

dist.run_commands()

File "/home/tic20/apps/chimerax/lib/python3.6/distutils/dist.py", line 955, in run_commands

self.run_command(cmd)

File "/home/tic20/apps/chimerax/lib/python3.6/distutils/dist.py", line 974, in run_command

cmd_obj.run()

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/setuptools/command/test.py", line 214, in run

installed_dists = self.install_dists(self.distribution)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/setuptools/command/test.py", line 205, in install_dists

ir_d = dist.fetch_build_eggs(dist.install_requires)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/setuptools/dist.py", line 453, in fetch_build_eggs

replace_conflicting=True,

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/pkg_resources/init.py", line 866, in resolve

replace_conflicting=replace_conflicting

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/pkg_resources/init.py", line 1146, in best_match

return self.obtain(req, installer)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/pkg_resources/init.py", line 1158, in obtain

return installer(requirement)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/setuptools/dist.py", line 520, in fetch_build_egg

return cmd.easy_install(req)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 666, in easy_install

raise DistutilsError(msg)

distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('Clipper-Python>=0.1')

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/chimerax/bundle_builder/bundle_builder.py", line 347, in _run_setup

setuptools.setup(kw)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/setuptools/init.py", line 129, in setup

return distutils.core.setup(attrs)

File "/home/tic20/apps/chimerax/lib/python3.6/distutils/core.py", line 163, in setup

raise SystemExit("error: " + str(msg))

SystemExit: error: Could not find suitable distribution for Requirement.parse('Clipper-Python>=0.1')
Traceback (most recent call last):

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/chimerax/core/commands/devel.py", line 151, in _run

unbound_method(bb, *args, kw)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/chimerax/bundle_builder/bundle_builder.py", line 15, in hack

return _func(*args, kw)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/chimerax/bundle_builder/bundle_builder.py", line 63, in make_install

self.make_wheel(test=test, debug=debug)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/chimerax/bundle_builder/bundle_builder.py", line 15, in hack

return _func(*args, kw)

File "/home/tic20/apps/chimerax/lib/python3.6/site-packages/chimerax/bundle_builder/bundle_builder.py", line 57, in make_wheel

raise RuntimeError("Building wheel failed")

RuntimeError: Building wheel failed

Executing: exit
Exiting ...
}}}

Yet when I manually install Clipper-Python via ChimeraX -m pip install ... it works fine, and then the ChimeraX Clipper plugin installs without complaint.

[tic20@dhcp-10-248-204-98 clipper]$ ChimeraX -m pip install clipper-python
Collecting clipper-python
  Using cached Clipper_Python-0.1.0-cp36-cp36m-manylinux1_x86_64.whl
Requirement already satisfied: numpy>=1.13.1 in /home/tic20/apps/chimerax/lib/python3.6/site-packages (from clipper-python)
Installing collected packages: clipper-python
Successfully installed clipper-python-0.1.0
Lock 140690030043768 acquired on /home/tic20/.cache/ChimeraX/0.1/toolshed/bundle_info.cache.lock
Lock 140690030043768 released on /home/tic20/.cache/ChimeraX/0.1/toolshed/bundle_info.cache.lock
[tic20@dhcp-10-248-204-98 clipper]$ ChimeraX -m pip install Clipper-Python
Requirement already satisfied: Clipper-Python in /home/tic20/apps/chimerax/lib/python3.6/site-packages
Requirement already satisfied: numpy>=1.13.1 in /home/tic20/apps/chimerax/lib/python3.6/site-packages (from Clipper-Python)
Lock 140375704882032 acquired on /home/tic20/.cache/ChimeraX/0.1/toolshed/bundle_info.cache.lock
Lock 140375704882032 released on /home/tic20/.cache/ChimeraX/0.1/toolshed/bundle_info.cache.lock

[Conrad Huang]

Has this been resolved with switching to using pip for all bundle installation?

[tic20@…]

No idea - I’m not actually pulling any dependencies from the PyPI these days, and haven’t been for some time now.
 

 

[Conrad Huang]

I think pulling from PyPI is working. If not, check #2013 which is about a similar issue.