How to fix Windows 8 Anaconda "can't open file" errors in cygwin when using absolute paths?

Question

I'm having troubles getting Anaconda to run python scripts on cygwin.

My configuration. Windows 8.1

$ echo $PATH
/usr/local/bin:/usr/bin:/cygdrive/c/WINDOWS/system32:/cygdrive/c/WINDOWS:/cygdrive/c/WINDOWS/System32/Wbem:/cygdrive/c/WINDOWS/Syste
m32/WindowsPowerShell/v1.0:/cygdrive/c/Anaconda:/cygdrive/c/Anaconda/Scripts

launching python or ipython with no script works fine:

$ which python
/cygdrive/c/Anaconda/python

$ python
Python 2.7.6 |Anaconda 1.9.2 (64-bit)| (default, Nov 11 2013, 10:49:15) [MSC v.1500 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()

$ ipython
Python 2.7.6 |Anaconda 1.9.2 (64-bit)| (default, Nov 11 2013, 10:49:15) [MSC v.1500 64 bit (AMD64)]
Type "copyright", "credits" or "license" for more information.

IPython 1.1.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]:
Do you really want to exit ([y]/n)? y

$ echo $PATH
/usr/local/bin:/usr/bin:/cygdrive/c/WINDOWS/system32:/cygdrive/c/WINDOWS:/cygdrive/c/WINDOWS/System32/Wbem:/cygdrive/c/WINDOWS/Syste
m32/WindowsPowerShell/v1.0:/cygdrive/c/Anaconda:/cygdrive/c/Anaconda/Scripts

Here's the problem:

$ pwd
/home/John

$ ls -l /cygdrive/c/cygwin64/home/John/FooDir/helloworld.py
-rwxrwx--x+ 1 John None 47 Apr 25 16:42 /cygdrive/c/cygwin64/home/John/FooDir/helloworld.py

$ cat /home/John/FooDir/helloworld.py
#!/usr/bin/env python
print("Hello, World!")

$ python FooDir/helloworld.py
Hello, World!

$ python /home/John/FooDir/helloworld.py
C:\Anaconda\python.exe: can't open file '/home/John/FooDir/helloworld.py': [Errno 2] No such file or directory

$ python /cygdrive/c/cygwin64/home/John/FooDir/helloworld.py
C:\Anaconda\python.exe: can't open file '/cygdrive/c/cygwin64/home/John/FooDir/helloworld.py': [Errno 2] No such file or directory

$ python C:\\Cygwin64\\home\\John\\FooDir\\helloworld.py
Hello, World!

This happens with any script that I try to run with absolute paths. I suspect the problem is caused by some sort of cygpath issue, but don't know how to fix it...

I don't have this problem when using Cygwin's version of python.

Answer 1

Cygwin performs a mapping between Windows paths and the paths that Cygwin programs see. For example, your Cygwin HOME directory /home/John is the Windows directory C:\cygwin\home\John. Putting the root of the Cygwin file system at the Windows C:\cygwin directory avoid collisions between Cygwin root directory names and Windows root directory names.

Cygwin also maps the root directories of Windows drives to directories under /cygdrive, so that Windows directories C:\ and D:\ are equivalent to Cygwin directories /cygdrive/c and /cygdrive/d.

Windows programs don't understand Cygwin absolute paths and Cygwin programs (generally) don't understand Windows absolute paths. You can convert between the two forms using the cygpath command. cygpath --help gives a pretty complete description of its capabilities.

Your Windows python program understands only Windows paths, so to get it to execute python /home/John/FooDir/helloworld.py, use cygpath like this:

python $(cygpath -w /home/John/FooDir/helloworld.py)

Or, knowing what you now know about the mapping between Cygwin paths and Windows paths, you could just run your Python script like this:

python "C:\cygwin\home\John\FooDir\helloworld.py"