Fix dictstrstr #1629
Fix dictstrstr #1629
Conversation
| @@ -33,7 +33,7 @@ | |||
| from traits.api import BaseUnicode | |||
| from traits.api import Unicode | |||
|
|
|||
| DictStrStr = traits.Dict(str, (bytes, str)) | |||
| DictStrStr = traits.Dict((bytes,str,unicode), (bytes,str,unicode)) | |||
There was a problem hiding this comment.
unicode does not exist in python 3 anymore.
you can do
import sys
DictStrStr = traits.Dict(str, (bytes,str))
if sys.version_info[0] < 3:
DictStrStr = traits.Dict((bytes,str,unicode), (bytes,str,unicode))
However, DictStrStr = traits.Dict((bytes, str), (bytes,str)) does not solve your problem as well?
There was a problem hiding this comment.
In the error, it seems that all my environ strings are in unicode, so without unicode it does not solve my problem.
There was a problem hiding this comment.
Maybe the solution is to typecast the environ somewhere in the base
interface class?
On Wed, Sep 14, 2016 at 9:00 AM, bpinsard [email protected] wrote:
In nipype/interfaces/traits_extension.py
#1629 (comment):@@ -33,7 +33,7 @@
from traits.api import BaseUnicode
from traits.api import Unicode-DictStrStr = traits.Dict(str, (bytes, str))
+DictStrStr = traits.Dict((bytes,str,unicode), (bytes,str,unicode))In the error, it seems that all my environ strings are in unicode, so
without unicode it does not solve my problem.—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/nipy/nipype/pull/1629/files/fce449863911f9512a69a35c2ae93eabb941ef8a#r78779207,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AAOkp3oMdKPi2qiLTGg8QpRyp9K2DvBKks5qqBopgaJpZM4J8Jid
.
There was a problem hiding this comment.
Does __future__ or something else is changing the environ content?
Because in any other context, the environ is all defined in str (=python3 bytes).
There was a problem hiding this comment.
Apparently, the problem is in the keys of environ, not the values.
Did it work for you using DictStrStr = traits.Dict((bytes, str), (bytes,str)) instead the version with unicode?
(i.e. adding bytes for the validation of keys in DictStrStr)
This should do (it worked on the SGE environment I created for testing, where I could reproduce the issue)
There was a problem hiding this comment.
Without unicode, it does not work, weirdly my os.environ is all unicode inside nipype, outside it regular python str.
What is weird, I removed my bashrc, then the bug is fixed, I also try to remove a lot of stuff from my bashrc and it is also fixed.
The bashrc is not utf8 coded, and does not contains any special character, so it might be some sourcing that introduce this bug.
So the interaction of these sourced bash scripts with nipype and future is causing os.environ to be all unicode in nipype only, why, I do not know?
Anyway, thanks for the help, I think we can keep the DictStrStr = traits.Dict((bytes, str), (bytes,str)) then ?
|
Ok just confirmed #1621 in a docker image with SGE. Also confirmed that |
Current coverage is 71.08% (diff: 100%)@@ master #1629 diff @@
==========================================
Files 1020 1020
Lines 51240 52343 +1103
Methods 0 0
Messages 0 0
Branches 7259 7645 +386
==========================================
+ Hits 36314 37206 +892
- Misses 13840 14030 +190
- Partials 1086 1107 +21
|
|
@bpinsard - it's possible that you have some environmental setup in bashrc that's affecting things. see: https://perlgeek.de/en/article/set-up-a-clean-utf8-environment also, there are lines like this, which can affect input: https://github.com/nipy/nipype/blob/master/nipype/interfaces/base.py#L1229 @oesteban - is |
|
@satra - yes, I think this patch is necessary. |
The future strings in traits definition causes crashes for most interfaces using os.environ as an input.