I'm not clear on the issue here, but generally LGTM. The change needs a test, and the commit message needs fixing, something like:

BUG: Savetxt may ignore newline character on Windows:

Extended explanation of problem...

Closes #3975.

Does loadtxt need a complimentary fix?

Sorry, I'm new to all this. Is there a quick-start-guide anywhere?
How can I commit a test? And can I edit the commit message to match your example?

loadtxt doesn't have a newline parameter, and therefore there's no need for a fix.

There is http://docs.scipy.org/doc/numpy/dev/, but is may not have what you are looking for.

To edit commit messages or squash commits for fixes, the easiest way it git rebase -i HEAD~n, where n is the number of commits you want to fix up. There are instructions that will come up when you do that, but for commit messages replace pick with r. After that you will need to force push git push --force origin whatever.

For tests, look to use existing tests as templates. The place for the test will be somewhere in numpy/lib/tests/test_io.py.

Thanks for your help.
I've just changed the commit message.

After looking at numpy/lib/tests/test_io.py I found the tests in class TestSaveTxt. Almost all of them check for a \n as line-separator but as the data is written to a BytesIO object and not a file, the bug was not detected. I'll now write my own test function.

Running my test with the unpatched version fails, as expected:

FAIL: test_newline (test_io.TestSaveTxt)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "numpy\lib\tests\test_io.py", line 433, in test_newline
    assert_equal(d, newline.join(['1', '2', '3', '']))
  File "numpy\ma\testutils.py", line 100, in assert_equal
    raise AssertionError(msg)
AssertionError: 
Items are not equal:
 ACTUAL: '1\r\n2\r\n3\r\n'
 DESIRED: '1\n2\n3\n'

With the patched version the test is passed, but 7 others fail:
test_1D, test_array, test_complex_arrays, test_delimiter, test_format, test_header_footer, test_record.
These test-function expect newline to be set to \n, that's the reason for those fails.

Possible solutions:

1. replacing os.linesep with \n in my patch
2. changing all tests to explicitly set newline to \n
3. replacing \n with os.linesep in all tests

What do you think?

@816-8055 Sorry for the long pause. I think the issues you raise would be best discussed on the mailing list before proceeding.

Cleanup at #5503, closing this. Thanks @816-8055 .