PyPI dependency fail on 'make app-install'

[Tristan Croll]

Pulls successfully from the repo in Linux, but on the Mac:

Tristans-MacBook-Air:clipper tic20$ make app-install
/Applications/ChimeraX.app/Contents/bin/ChimeraX --nogui --cmd "devel install . ; exit"
0.00% done: Initializing core
50.00% done: Initializing bundles
Executing: devel install . 
running build
running build_py
running build_ext
running test
Searching for Clipper-Python>=0.1.1
Reading https://pypi.python.org/simple/Clipper-Python/
Download error on https://pypi.python.org/simple/Clipper-Python/: [SSL: TLSV1_ALERT_PROTOCOL_VERSION] tlsv1 alert protocol version (_ssl.c:777) -- Some packages may not be found!
Couldn't find index page for 'Clipper-Python' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.python.org/simple/
Download error on https://pypi.python.org/simple/: [SSL: TLSV1_ALERT_PROTOCOL_VERSION] tlsv1 alert protocol version (_ssl.c:777) -- Some packages may not be found!
No local packages or working download links found for Clipper-Python>=0.1.1
Traceback (most recent call last):
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 955, in run_commands
    self.run_command(cmd)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/setuptools/command/test.py", line 214, in run
    installed_dists = self.install_dists(self.distribution)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/setuptools/command/test.py", line 205, in install_dists
    ir_d = dist.fetch_build_eggs(dist.install_requires)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/setuptools/dist.py", line 480, in fetch_build_eggs
    replace_conflicting=True,
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 881, in resolve
    replace_conflicting=replace_conflicting
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1164, in best_match
    return self.obtain(req, installer)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1176, in obtain
    return installer(requirement)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/setuptools/dist.py", line 547, in fetch_build_egg
    return cmd.easy_install(req)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 667, in easy_install
    raise DistutilsError(msg)
distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('Clipper-Python>=0.1.1')

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/bundle_builder/bundle_builder.py", line 347, in _run_setup
    setuptools.setup(**kw)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/setuptools/__init__.py", line 129, in setup
    return distutils.core.setup(**attrs)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/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>=0.1.1')
Traceback (most recent call last):
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/devel.py", line 151, in _run
    unbound_method(bb, *args, **kw)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/bundle_builder/bundle_builder.py", line 15, in hack
    return _func(*args, **kw)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/bundle_builder/bundle_builder.py", line 63, in make_install
    self.make_wheel(test=test, debug=debug)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/bundle_builder/bundle_builder.py", line 15, in hack
    return _func(*args, **kw)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/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 ...

But if I install via ChimeraX -m pip install Clipper-Python:

Tristans-MacBook-Air:clipper tic20$ ChimeraX -m pip install Clipper-Python
Collecting Clipper-Python
  Downloading https://files.pythonhosted.org/packages/59/95/78fa7a84722f5429662c1dae31305af5fbf4e120f180d458a8622bbc8411/Clipper_Python-0.1.1-cp36-cp36m-macosx_10_6_intel.whl (34.6MB)
    100% |████████████████████████████████| 35.0MB 36kB/s 
Requirement already satisfied: numpy>=1.14.0 in /Applications/ChimeraX.app/Contents/lib/python3.6/site-packages (from Clipper-Python)
Installing collected packages: Clipper-Python
Successfully installed Clipper-Python-0.1.1
You are using pip version 9.0.3, however version 10.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Lock 4471280752 acquired on /Users/tic20/Library/Caches/ChimeraX/0.6/toolshed/bundle_info.cache.lock
Lock 4471280752 released on /Users/tic20/Library/Caches/ChimeraX/0.6/toolshed/bundle_info.cache.lock
Tristans-MacBook-Air:clipper tic20$ 

... and everything works fine from that point on.

[Conrad Huang]

Hi, Tristan.

Have you tried this with the latest daily build? One of the issues addressed recently is that PyPI is now refusing connections with SSL protocols earlier than TLS 1.2. As you can see in the output:

Searching for Clipper-Python>=0.1.1
Reading https://pypi.python.org/simple/Clipper-Python/
Download error on https://pypi.python.org/simple/Clipper-Python/: [SSL: TLSV1_ALERT_PROTOCOL_VERSION] tlsv1 alert protocol version (_ssl.c:777) -- Some packages may not be found!
Couldn't find index page for 'Clipper-Python' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.python.org/simple/
Download error on https://pypi.python.org/simple/: [SSL: TLSV1_ALERT_PROTOCOL_VERSION] tlsv1 alert protocol version (_ssl.c:777) -- Some packages may not be found!
No local packages or working download links found for Clipper-Python>=0.1.1

I'm not sure why it is LOOKING for Clipper-Python 0.1.1 at PyPI, but that's a separate symptom. Can you please try with the latest daily build and let me know the results? Thanks.

Conrad

[tic20@…]

I can’t (yet). I’m releasing this ISOLDE build for ChimeraX 0.6 - after that, I’ll need to make a number of changes to make it compatible with 0.7’s changes to Drawing. 

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

[Conrad Huang]

Well, at least you have a workaround. The change was on the PyPI and and ChimeraX has to be changed in order to accommodate that change.

[Greg Couch]

Using newer OpenSSL now.