py-obspy: Incorrect permissions on [..]/site-packages/obspy/taup/data

[anowacki (Andy Nowacki)]

ObsPy (as of trunk r137599) has a problem with file permissions. Specifically, the code requires read access to the following files and directories by a normal user, but they are currently set as readable only by root:wheel:

1. ${prefix}/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy-0.10.2-py2.7.egg-info

   $ ls -l /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy-0.10.2-py2.7.egg-info/
   total 160
   -rw-------  1 root  wheel   2611 19 May 20:28 PKG-INFO
   -rw-------  1 root  wheel  47494 19 May 20:28 SOURCES.txt
   -rw-------  1 root  wheel      1 19 May 20:28 dependency_links.txt
   -rw-------  1 root  wheel   7552 19 May 20:28 entry_points.txt
   -rw-------  1 root  wheel      1 19 May 20:28 namespace_packages.txt
   -rw-------  1 root  wheel      1 15 May 19:36 not-zip-safe
   -rw-------  1 root  wheel    141 19 May 20:28 requires.txt
   -rw-------  1 root  wheel    166 19 May 20:28 top_level.txt
   

This directory sometimes itself lacks execution permission for all users, but I could not reliably reproduce this when uninstalling and installing ObsPy to test.

2. ${prefix}/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/data

   $ ls -l /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/data
   total 616
   -rw-------  1 root  wheel      81 15 May 19:31 README.txt
   -rw-------  1 root  wheel  144910 15 May 19:31 ak135.npz
   -rw-------  1 root  wheel    6413 15 May 19:31 ak135.tvel
   -rw-------  1 root  wheel  145978 15 May 19:31 iasp91.npz
   -rw-------  1 root  wheel    5761 15 May 19:31 iasp91.tvel
   

The code below shows both the errors and my interim fix.

$ cat /tmp/test.py
from obspy.taup import TauPyModel
m = TauPyModel()
$ 
$ python2.7 /tmp/test.py && echo success
Traceback (most recent call last):
  File "/tmp/test.py", line 1, in <module>
    from obspy.taup import TauPyModel
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/__init__.py", line 36, in <module>
    from obspy.core.utcdatetime import UTCDateTime  # NOQA
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/core/__init__.py", line 107, in <module>
    from obspy.core.util.attribdict import AttribDict
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/core/util/__init__.py", line 40, in <module>
    from obspy.core.util.obspy_types import (ComplexWithUncertainties, Enum,
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/core/util/obspy_types.py", line 16, in <module>
    with standard_library.hooks():
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/future/standard_library/__init__.py", line 323, in __enter__
    install_hooks()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/future/standard_library/__init__.py", line 528, in install_hooks
    install_aliases()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/future/standard_library/__init__.py", line 482, in install_aliases
    import test
  File "/private/tmp/test.py", line 2, in <module>
    m = TauPyModel()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/tau.py", line 317, in __init__
    self.model = TauModel.from_file(model)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/tau_model.py", line 600, in from_file
    return TauModel.deserialize(filename)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/tau_model.py", line 520, in deserialize
    npz = np.load(filename)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/npyio.py", line 369, in load
    fid = open(file, "rb")
IOError: [Errno 13] Permission denied: u'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/data/iasp91.npz'
$ 
$ sudo chmod a+r /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy-0.10.2-py2.7.egg-info/*
$ python2.7 /tmp/test.py && echo success
Traceback (most recent call last):
  File "/tmp/test.py", line 1, in <module>
    from obspy.taup import TauPyModel
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/__init__.py", line 36, in <module>
    from obspy.core.utcdatetime import UTCDateTime  # NOQA
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/core/__init__.py", line 107, in <module>
    from obspy.core.util.attribdict import AttribDict
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/core/util/__init__.py", line 40, in <module>
    from obspy.core.util.obspy_types import (ComplexWithUncertainties, Enum,
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/core/util/obspy_types.py", line 16, in <module>
    with standard_library.hooks():
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/future/standard_library/__init__.py", line 323, in __enter__
    install_hooks()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/future/standard_library/__init__.py", line 528, in install_hooks
    install_aliases()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/future/standard_library/__init__.py", line 482, in install_aliases
    import test
  File "/private/tmp/test.py", line 2, in <module>
    m = TauPyModel()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/tau.py", line 317, in __init__
    self.model = TauModel.from_file(model)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/tau_model.py", line 600, in from_file
    return TauModel.deserialize(filename)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/tau_model.py", line 520, in deserialize
    npz = np.load(filename)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/npyio.py", line 369, in load
    fid = open(file, "rb")
IOError: [Errno 13] Permission denied: u'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/data/iasp91.npz'
$ 
$ sudo chmod a+x /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/data
$ sudo chmod a+r /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/obspy/taup/data/*
$ python2.7 /tmp/test.py && echo success
success

My apologies for not presenting a patch to fix this, but I doubt that just adding the chmod commands would be a satisfactory fix.

[petrrr]

This should be fixed by r137702. Please selfupdate and upgrade the port.

[petrrr]

And r137704 replaces the ugly construct due to my poor TCL knowledge. Thanks Lawrence!