[FIXED] Anaconda and Spyder won't open if PythonPath is set

Issue

I'm new to using Anaconda and Spyder and this must be a simple setting issue, but it's really frustrating. I need to have a PythonPath environment set because I frequently run scripts in ArcGIS which won't work without a path. However, neither Anaconda Navigator nor Spyder will not open if there is a PythonPath set. I get the splash screen, but that's it, it doesn't open. If I remove the PythonPath and reboot, Anaconda and Spyder work, but not ArcGIS. This is not an ArcGIS problem, rather Anaconda and Spyder just don't seem to like there being a PythonPath at all. Anyone have experience with this?

For reference, my PythonPath contains:

C:\Python27;
C:\Python27\Lib;
C:\Python27\Lib\site-packages;
C:\Python27\DLLs;
C:\Python27\Lib\lib-tk;
C:\Python27\scripts;
C:\Python27\ArcGIS10.3\Lib;
C:\Python27\ArcGIS10.3\Lib\lib-tk;
C:\Python27\ArcGIS10.3\Lib\site-packages;
C:\Program Files (x86)\ArcGIS\Desktop10.3\arcpy;
C:\Program Files (x86)\ArcGIS\Desktop10.3\bin

I can remove everything except the bottom five and ArcGIS scripts still work, but it doesn't fix the problem with Spyder. It probably has something to do with the files not actually being executables, but links to scripts. For example, the shortcut for Spyder points to:

C:\ProgramData\Anaconda2\pythonw.exe C:\ProgramData\Anaconda2\cwp.py C:\ProgramData\Anaconda2 "C:/ProgramData/Anaconda2/pythonw.exe" "C:/ProgramData/Anaconda2/Scripts/spyder-script.py"

which seems to leave a lot of room for trouble. Interestingly, if I run from the Command Prompt, the first time there are no errors but nothing happens, and the second time it displays:

Spyder is already running. If you want to open a new instance, please pass to it the --new-instance option

Solution

You seem to have relic python installation kicking around and it wasn't uninstalled prior to installing ArcMap. The correct path structure for a clean installation of ArcMap with its associated python would consist of

C:\Python27\ArcGISxx.x

and there are no other files or folders in the C:\Python27 path. I would suggest uninstalling python completely and do a 'repair' of the arcmap distribution which will reinstall python and its dependencies correctly. In the interim, you should move the last 3 lines (which refer to arcmap) to the top of the dependency list. That may resolve things temporarily.

Answered By - NaN