Environment is Ubuntu 12.x LTS 64 bit. I ran the install as follows :
sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose
Everything installed great, and I tried out the 'getting started' example only to come upon this error as if my env. is't set correctly..
See orig # http://www.scipy.org/getting-started.html
usernamep#ubuntudev:~$ ipython --pylab
Python 2.7.3 (default, Sep 26 2013, 20:03:06)
Type "copyright", "credits" or "license" for more information.
IPython 0.12.1 -- 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.
Welcome to pylab, a matplotlib-based Python environment [backend: TkAgg].
For more information, type 'help(pylab)'.
In [1]: from scipy import special, optimize
In [2]: f = lambda x: -special.jv(3,x)
In [3]: sol = optimize.minimize(f, 1.0)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/user/<ipython-input-3-ea43eb308d3c> in <module>()
----> 1 sol = optimize.minimize(f, 1.0)
AttributeError: 'module' object has no attribute 'minimize'
In [4]:
Do I need to reform their example's import? Checking their docs now...
optimize.minimize was introduced in Scipy v.0.11 (see http://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.minimize.html ).
On Debian, that would mean that you need Jessie or better. On Ubuntu, you appear to need raring or better.
Almost certainly the scipy you installed using apt-get is simply too old to have minimize: (0.10, I'd guess). The code works for me:
>>> from scipy import special, optimize
>>> def f(x): return -special.jv(3,x)
>>> sol = optimize.minimize(f, 1.0)
>>> sol
status: 0
success: True
njev: 17
nfev: 51
hess_inv: array([[ 4.70024446]])
fun: -0.43439442684052476
x: array([ 4.20118891])
message: 'Optimization terminated successfully.'
jac: array([ -3.72529030e-09])
I think you'll be better off using pip to install the stack.
python-scipy package in the Ubuntu 12 is a bit old. I think it is ver 0.9.0. The optimize.minimize function was added to scipy ver 0.11.0.
Related
I have anaconda python3 kernel with pytorch and numpy installed in the environment. In jupyter notebook first line 'import torch' produces error.
I am using anaconda navigator to launch jupyter notebook and enter my environment and see pytorch is installed but not being imported. Tried various dir extensions 'from torch... import * but more error
import torch
ImportError Traceback (most recent call last)
<ipython-input-1-20507c95d9af> in <module>
1
----> 2 import torch
3
4
~/anaconda3/envs/udacity1/lib/python3.6/site-packages/torch/__init__.py in <module>
100 pass
101
--> 102 from torch._C import *
103
104 __all__ += [name for name in dir(_C)
ImportError: /home/frida/anaconda3/envs/udacity1/lib/python3.6/site-packages/torch/lib/libtorch.so.1: undefined symbol: nvrtcGetProgramLogSize
I was able to add this to the end of my path to establish a 'backend ' for my notebook kernel. Thanks to Kris Stern!
-m ipykernel install --user
first get your kernel path with
(which python3)
then connect it using
sudo (your path)/anaconda3/bin/python3 -m ipykernel install --user
I'm trying to get ipython style table complete with pdb by using ipdb.
On a clean ubuntu 14.04 install (new aws instance) I run.
sudo apt-get update
sudo apt-get upgrade -y
sudo apt-get install python-setuptools
sudo easy_install pip
sudo pip install ipython
sudo pip install ipdb
sudo pip install boto
Then boot up ipython, and try.
ubuntu#ip-10-0-0-244:~$ ipython
Python 2.7.6 (default, Mar 22 2014, 22:59:56)
Type "copyright", "credits" or "license" for more information.
IPython 2.3.1 -- 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]: import ipdb
In [2]: import boto
In [3]: ipdb.set_trace()
--Call--
> /usr/local/lib/python2.7/dist-packages/IPython/core/displayhook.py(234)__call__()
233
--> 234 def __call__(self, result=None):
235 """Printing with history cache management.
ipdb> str.
str.capitalize str.encode str.format str.isdigit str.isupper str.lstrip str.rfind str.rsplit str.startswith str.translate
str.center str.endswith str.index str.islower str.join str.mro str.rindex str.rstrip str.strip str.upper
str.count str.expandtabs str.isalnum str.isspace str.ljust str.partition str.rjust str.split str.swapcase str.zfill
str.decode str.find str.isalpha str.istitle str.lower str.replace str.rpartition str.splitlines str.title
ipdb> boto.
boto.[tab] just sits there. If I'm reading the docs right this should work, but maybe I have miss-understood something.
If I define a simple script test.py
import boto
print(boto.__version__)
Then call:
ubuntu#ip-10-0-0-244:~$ python -m ipdb test.py
> /home/ubuntu/test.py(1)<module>()
----> 1 import boto
2
3 print(boto.__version__)
ipdb> n
> /home/ubuntu/test.py(3)<module>()
1 import boto
2
----> 3 print(boto.__version__)
ipdb> boto.
boto.BUCKET_NAME_RE boto.connect_autoscale boto.connect_emr boto.connect_s3 boto.os
boto.BotoConfigLocations boto.connect_beanstalk boto.connect_euca boto.connect_sdb boto.perflog
boto.BucketStorageUri boto.connect_cloudformation boto.connect_fps boto.connect_ses boto.platform
boto.Config boto.connect_cloudfront boto.connect_glacier boto.connect_sns boto.plugin
boto.ENDPOINTS_PATH boto.connect_cloudsearch boto.connect_gs boto.connect_sqs boto.pyami
boto.FileStorageUri boto.connect_cloudsearch2 boto.connect_ia boto.connect_sts boto.re
boto.GENERATION_RE boto.connect_cloudtrail boto.connect_iam boto.connect_support boto.regioninfo
boto.InvalidUriError boto.connect_cloudwatch boto.connect_kinesis boto.connect_swf boto.resultset
boto.NullHandler boto.connect_cognito_identity boto.connect_logs boto.connect_vpc boto.s3
boto.TOO_LONG_DNS_NAME_COMP boto.connect_cognito_sync boto.connect_mturk boto.connect_walrus boto.set_file_logger
boto.UserAgent boto.connect_directconnect boto.connect_opsworks boto.datetime boto.set_stream_logger
boto.VERSION_RE boto.connect_dynamodb boto.connect_rds boto.exception boto.storage_uri
boto.Version boto.connect_ec2 boto.connect_rds2 boto.handler boto.storage_uri_for_key
boto.boto boto.connect_ec2_endpoint boto.connect_redshift boto.init_logging boto.sys
boto.compat boto.connect_elastictranscoder boto.connect_route53 boto.log boto.urlparse
boto.config boto.connect_elb boto.connect_route53domains boto.logging boto.vendored
I get the behavior I'd like.
Does anyone know how to make the tab complete functionality work for the set_trace() work case?
-Thanks
I am using Enthought's Canopy environment on a 64 bit Linux OS. Everything works fine in the Ipython console which is attached with the editor. But when I ipython in the terminal and try to use magic functions, I get the following error.
---------------------------------------------------------------------------
error Traceback (most recent call last)
<ipython-input-3-29a4050aa687> in <module>()
----> 1 get_ipython().show_usage()
/home/shahensha/Development/Canopy/appdata/canopy-1.0.3.1262.rh5-x86_64/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in show_usage(self)
2931 def show_usage(self):
2932 """Show a usage message"""
-> 2933 page.page(IPython.core.usage.interactive_usage)
2934
2935 def extract_input_lines(self, range_str, raw=False):
/home/shahensha/Development/Canopy/appdata/canopy-1.0.3.1262.rh5-x86_64/lib/python2.7/site-packages/IPython/core/page.pyc in page(strng, start, screen_lines, pager_cmd)
188 if screen_lines <= 0:
189 try:
--> 190 screen_lines += _detect_screen_size(screen_lines_def)
191 except (TypeError, UnsupportedOperation):
192 print(str_toprint, file=io.stdout)
/home/shahensha/Development/Canopy/appdata/canopy-1.0.3.1262.rh5-x86_64/lib/python2.7/site-packages/IPython/core/page.pyc in _detect_screen_size(screen_lines_def)
112 # Proceed with curses initialization
113 try:
--> 114 scr = curses.initscr()
115 except AttributeError:
116 # Curses on Solaris may not be complete, so we can't use it there
/home/shahensha/Development/Canopy/appdata/canopy-1.0.3.1262.rh5-x86_64/lib/python2.7/curses/__init__.pyc in initscr()
31 # instead of calling exit() in error cases.
32 setupterm(term=_os.environ.get("TERM", "unknown"),
---> 33 fd=_sys.__stdout__.fileno())
34 stdscr = _curses.initscr()
35 for key, value in _curses.__dict__.items():
error: setupterm: could not find terminfo database
So, I installed a bare bones iPython shell which is not the one provided by Canopy and tried the same magic functions in there and it works fine.
Have I done something wrong with the installation? Please help
Thanks a lot
shahensha
This is not a solution, but just an observation. My desktop is MacOS-X and I connect to a Centos machine to run Enthought Canopy both 64 bit. I get the same error message as OP if I ssh from iterm2, but not if I use the Terminal app.
I am not sure what the underlying reason is, but may be someone can verify if a similar situation is true for linux. Interestingly I can use either iterm2 or Terminal on the local canopy without any issues.
Update:
I just noticed that the TERM environment variable in iterm2 was set to "xterm" while the Terminal app was showing "xterm-256color". Issuing the command export TERM="xterm-256color" before running the Canopy ipython in terminal solves the issue for me in iterm2.
Problem reproduction:
$ python -c 'import curses; curses.setupterm()'
Traceback (most recent call last):
File "<string>", line 1, in <module>
_curses.error: setupterm: could not find terminfo database
This irc log gave me the idea that this error was to do with libncursesw.
My Canopy version is 1.0.3.1262.rh5-x86_64. I have installed it to ~/src/canopy.
In ~/src/canopy/appdata/canopy-1.0.3.1262.rh5-x86_64/lib we can see that my canopy install has libncursesw.so.5.7.
My machine (Debian Wheezy 64bit) has libncursesw.so.5.9 (in /lib/x86_64-linux-gnu/libncursesw.so.5.9). I made canopy use this. You can toggle the problem on / off by using LD_PRELOAD and pointing at the .so file.
Solution
Replace libncurses.so.5.7 with libncurses.so.5.9:
CANOPYDIR=$HOME/src/canopy
CANOPYLIBS=$CANOPYDIR/appdata/canopy-1.0.3.1262.rh5-x86_64/lib/
SYSTEMLIBS=/lib/x86_64-linux-gnu
cp $SYSTEMLIBS/libncurses.so.5.9 $CANOPYLIBS
ln -sf $CANOPYLIBS/libncurses.so.5.9 $CANOPYLIBS/libncurses.so.5
It appears that Canopy User Python is not your default. See this article:
https://support.enthought.com/entries/23646538-Make-Canopy-s-Python-be-your-default-Python-i-e-on-the-PATH-
Update: Not true here -- instead, see batu's workaround answer.
I opened a picture with PIL, but when I tried to use split() to split the channels I got following error:
AttributeError: 'NoneType' object has no attribute 'bands'
import Image
img = Image.open('IMG_0007.jpg')
img.split()
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/blum/<ipython console> in <module>()
/usr/lib/python2.6/dist-packages/PIL/Image.pyc in split(self)
1495 "Split image into bands"
1496
-> 1497 if self.im.bands == 1:
1498 ims = [self.copy()]
1499 else:
AttributeError: 'NoneType' object has no attribute 'bands'
With googling I found this comment on SO, stating that PIL is sometimes 'lazy' and 'forgets' to load after opening. So you have to do it like this:
import Image
img = Image.open('IMG_0007.jpg')
img.load()
img.split()
Please +1 also the original comment! This person did the real work.
My problem was that PIL was not installed correctly. When trying to read a png I'd get that error. My compilation summary yielded
--------------------------------------------------------------------
PIL 1.1.7 SETUP SUMMARY
--------------------------------------------------------------------
version 1.1.7
platform linux2 2.7.3 (default, Apr 21 2012, 01:05:55)
[GCC 4.6.3]
--------------------------------------------------------------------
*** TKINTER support not available
*** JPEG support not available
*** ZLIB (PNG/ZIP) support not available <===============
*** FREETYPE2 support not available
*** LITTLECMS support not available
--------------------------------------------------------------------
I then opted to "pip uninstall pil" and used the Synaptic Package Manager instead. That fixed it.
After installing Ming 0.3.2, I tested the installation by running the following code:
>>> from ming.datastore import DataStore
>>> bind = DataStore('mongodb://localhost:27017/', database='tutorial')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: __init__() got an unexpected keyword argument 'database'
>>> ^D
I looked at the installation files and in the datastore.py file I found that the class's constructor did not contain a "database" argument.
class DataStore(object):
def __init__(self, bind, name, authenticate=None):
self.bind = bind
self.name = name
self._authenticate = authenticate
self._db = None
I then installed Ming 0.3.0 to look at the datastore.py file and found the DataStore class to match the documentation (it contained a database arg) and then tried that version where I encountered other complications.
I use easy_install to install Ming and I have a good install of mongodb and pymongo running. I run these on OS X Lion. Any advise on getting Ming running would be appreciated.
I think there may be a conflict with the newest version of pymongo and ming.
bind = DataStore('mongodb://localhost:27017/', name='test') gets me a bit further along, but I ended up just using pymongo by itself.
I've met the same issue. Here are the steps I've tried, and it works! Hopes it works for your environment too.
Uninstall the Ming 0.3.2 version by : pip uninstall Ming
Install 0.3.0 by: pip install -Iv http://downloads.sourceforge.net/project/merciless/0.3.0/Ming-0.3.0.tar.gz
Try the example on the Ming office website again. There will be another error
Traceback (most recent call last):
File "tutorial.py", line 1, in <module>
from ming.datastore import DataStore
File "/home/me/work/deploy/test/local/lib/python2.7/site-packages/ming/init.py", line 3, in <module>
from session import Session
File "/home/me/work/deploy/test/local/lib/python2.7/site-packages/ming/session.py", line 7, in <module>
from pymongo.son import SON
ImportError: No module named son
change the line 7 of "/home/me/work/deploy/test/local/lib/python2.7/site-packages/ming/session.py" to from bson.son import SON
try again. and it will works.
Here is the link I've referenced. It's a Japanese webpage, but you can translate it to English by google translator.
http://ryooo321.blogspot.com/2012/05/macsleepymongoose.html
try to remove database=.
In [8]: from ming.datastore import DataStore
In [9]: bind = DataStore('mongodb://grid:27017/', 'tutorial')
In [10]: bind.name
Out[10]: 'tutorial'