fix os.symlink call for gather_templates --structure_paths - use abspath

[rafwiewiora]

Fixes https://github.com/choderalab/ensembler/issues/73

(that's adding a trailing new line at the end in the diff)

[jchodera]

Can you add a corresponding test to catch the original problem this was designed to solve?

[jchodera]

To get the travis tests to run, you'll have to change this line from Miniconda-latest-Linux to Miniconda2-latest-Linux.

[jchodera]

Nevermind, I fixed this in #75

[rafwiewiora]

re test: there was one already (https://github.com/choderalab/ensembler/blob/master/ensembler/tests/test_initproject.py#L101) but that uses the absolute path, hence works.

If I want to test using a relative path - do I have guarantee that the current folder will always be the folder in which the test script sits? Not sure how Travis works with that kind of thing.

[jchodera]

If I want to test using a relative path - do I have guarantee that the current folder will always be the folder in which the test script sits? Not sure how Travis works with that kind of thing.

I would write a test that does the following:

• Create a temporary directory with tempfile.mkdtemp()
• Store the original (current) working directory
• Change to the temporary directory
• copy from structure_paths = [get_installed_resource_filename(os.path.join('tests', 'resources'))]
• run the test using the local directory
• Make sure to restore the original working directory even if an exception is thrown

[rafwiewiora]

Thanks! Test added.

[jchodera]

We're still working on fixing tests---sorry! See #80

[rafwiewiora]

No problem!