I have a package called 'Prody' which is installed under anaconda directories:
$ python
Python 2.7.8 |Anaconda 2.0.1 (x86_64)| (default, Jul 2 2014, 15:36:00)
[GCC 4.2.1 (Apple Inc. build 5577)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
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>>> import prody
>>> prody.__file__
'//anaconda/lib/python2.7/site-packages/ProDy-1.5.1-py2.7-macosx-10.5-x86_64.egg/prody/__init__.pyc'
I'd like to remove that file with this command but failed:
$ conda remove prody
Error: no packages found to remove from environment: //anaconda
What's the right way to do it?
You can remove packages installed with pip using pip uninstall.
Did you install Prody via pip? Then I don't think that conda remove can remove it. AFAIK, conda manages only conda packages.
Related
Here is an extract of my console in a Mac, as you can see the Python on the console is 2.7.15 but on the environment it becomes 2.7.10 which is an older version... any help on why and how to fix it would be most welcomed!
dhcp-18-57:Wakeup6 **jbs$ python**
**Python 2.7.15** (default, May 1 2018, 16:44:14)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()
dhcp-18-57:Wakeup6 jbs$ virtualenv env
New python executable in /Users/jbs/PycharmProjects/Wakeup6/env/bin/python
Installing setuptools, pip, wheel...done.
dhcp-18-57:Wakeup6 jbs$ source env/bin/activate
(env) dhcp-18-57:Wakeup6 **jbs$ python**
**Python 2.7.10** (default, Oct 23 2015, 19:19:21)
[GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()
If you installed python using Anaconda, then set up a new virtual environment for python 2.7.15 Then following directions in the Anaconda documentation, activate this virtual environment and you should be good to go.
If you didn't use Anaconda, just follow the directions for setting up a virtual environment on a Unix box. Then activate that environment and start working.
You can have multiple versions on your computer. Virtual environments allow you to run the version you want. I have virtual environments for python 2.7.13 and python 3.6.
If this doesn't work please let me know. I'll try to help.
Thank you all for your input. I finally figured out how to solve it. The difficult part was finding out how to locate the place where python 2.7.15 was installed which I'll leave intact in the response since I found it by trial and error looking in other places. I have not found a command that gives you the full path (perhaps an expert can tell us how to go from the laconic which python to the full path).
What I find interesting is that it does not really matter what the console uses when calling virtualenv. What matters is the version of Python used to install virtualenv which is the default version that will be used.
Essentially one has to use the -p option in virtualenv and make sure to find the right location where the desired version of python is.
dhcp-18--41:WakeUp8 jbs$ virtualenv -p /usr/local/Cellar/python#2/2.7.15/bin/python env
Running virtualenv with interpreter /usr/local/Cellar/python#2/2.7.15/bin/python
New python executable in /Users/jbs/PycharmProjects/WakeUp8/env/bin/python2.7
Also creating executable in /Users/jbs/PycharmProjects/WakeUp8/env/bin/python
Installing setuptools, pip, wheel...done.
dhcp-18-189-34-41:WakeUp8 jbs$ python
Python 2.7.15 (default, May 1 2018, 16:44:14)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()
dhcp-18--41:WakeUp8 jbs$ pwd
/Users/jbs/PycharmProjects/WakeUp8
dhcp-18-189-34-41:WakeUp8 jbs$ source env/bin/activate
(env) dhcp-18-189-34-41:WakeUp8 jbs$ python
Python 2.7.15 (default, May 1 2018, 16:44:14)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
I am using anaconda on mac-osx and have installed python-igraph. Currently not being able to import igraph.
Below is the error shown:
Python 2.7.12 |Anaconda 4.1.1 (x86_64)|
import igraph ----
ImportError: No module named igraph
It is present in this path - /Users/pc_name/anaconda/lib/python2.7/site-packages and I find only python_igraph-0.7.1.post6-py2.7.egg-info file.
I tried many things possible which are available on the other questions here at stack overflow. How can I solve this problem?
I used the following command and it worked for me in Python 3.7
pip install python-igraph
The detail about the package and its installation can be found
https://igraph.org/python/
You haven't mentioned how you installed python-igraph so it's hard to say anything. But I'm pretty sure that this package works nicely.
1)While in the python-igraph-master directory on my computer run the following:
conda install -c marufr python-igraph
2)In a new terminal window kick start python:
$python
Python 2.7.13 |Anaconda 4.3.1 (x86_64)| (default, Dec 20 2016, 23:05:08)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import igraph
>>>
I hope this helps
I run into this issue ImportError numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS2_AsASCIIString installing Python in a pyenv-virtualenv environment.
In my case, it happens with the matplotlib package instead of numpy (as in the above question), but it's basically the same issue.
The answer given in that question is a simple:
Rebuild NumPy against a Python built as UCS-4.
I don't know how to do this. In this other question it is said that one has to use:
./configure --enable-unicode=ucs4
but I don't know how to use that command along with pyenv.
This issue is also mentioned in pyenv's repo issue list, and a solution given in a comment. Sadly (for me) I can not understand how to apply the fix explained in said comment.
So my question basically is: how do I build Python as UCS-4 via pyenv?
Installing python with pyenv with ucs2:
$ export PYTHON_CONFIGURE_OPTS=--enable-unicode=ucs2
$ pyenv install -v 2.7.11
...
$ pyenv local 2.7.11
$ pyenv versions
system
* 2.7.11 (set by /home/nwani/.python-version)
$ /home/nwani/.pyenv/shims/python
Python 2.7.11 (default, Aug 13 2016, 13:42:13)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sysconfig
>>> sysconfig.get_config_vars()['CONFIG_ARGS']
"'--prefix=/home/nwani/.pyenv/versions/2.7.11' '--enable-unicode=ucs2' '--libdir=/home/nwani/.pyenv/versions/2.7.11/lib' 'LDFLAGS=-L/home/nwani/.pyenv/versions/2.7.11/lib ' 'CPPFLAGS=-I/home/nwani/.pyenv/versions/2.7.11/include '"
Installing python with pyenv with ucs4:
$ pyenv uninstall 2.7.11
pyenv: remove /home/nwani/.pyenv/versions/2.7.11? y
$ export PYTHON_CONFIGURE_OPTS=--enable-unicode=ucs4
$ pyenv install -v 2.7.11
...
$ pyenv local 2.7.11
$ pyenv versions
system
* 2.7.11 (set by /home/nwani/.python-version)
$ /home/nwani/.pyenv/shims/python
Python 2.7.11 (default, Aug 13 2016, 13:49:09)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sysconfig
>>> sysconfig.get_config_vars()['CONFIG_ARGS']
"'--prefix=/home/nwani/.pyenv/versions/2.7.11' '--enable-unicode=ucs4' '--libdir=/home/nwani/.pyenv/versions/2.7.11/lib' 'LDFLAGS=-L/home/nwani/.pyenv/versions/2.7.11/lib ' 'CPPFLAGS=-I/home/nwani/.pyenv/versions/2.7.11/include '"
I've tried many ways to install scipy but without successes. I use virtualenv on Linux Mate.
After the workon command I tried
pip install scipy
or
easy_install scipy
end every time is a "failed with exit status 1"
I tried also
apt-get install python-scipy
and I've no errors but if I run python
python
import scipy
I'll have "ImportError: No module named scipy"
What is wrong?
I'd suggest using Miniconda to install scipy.
wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b
Then, create a Conda environment with scipy installed:
conda create -n scipy scipy
Now you'll have access to the activate and deactivate scripts, used to open and close Conda environments.
$ source activate scipy
discarding /Users/username/miniconda/bin from PATH
prepending /Users/username/miniconda/envs/scipy/bin to PATH
(scipy)$ python
Python 2.7.11 |Continuum Analytics, Inc.| (default, Dec 6 2015, 18:57:58)
[GCC 4.2.1 (Apple Inc. build 5577)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import scipy
>>> scipy.version.version
'0.16.0'
[Edit] You indicated you want to use the system installed scipy package, that you have successfully installed via apt, in a virtualenv. You can instruct virtualenv to create a new environment that includes all the system Python packages like this:
$ virtualenv --system-site-packages scipy_env
New python executable in scipy_env/bin/python
Installing setuptools, pip...done.
$ source scipy_env/bin/activate
(scipy_env)$ python
Python 2.7.10 (default, Jul 14 2015, 19:46:27)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
Working inside a virtualenv, I'm trying to install scikit-image, but it fails, telling me that I need a newer (or any) version of numpy.
$ sudo pip install -U scikit-image
...
ImportError: You need `numpy` version 1.6 or later.
----------------------------------------
Command python setup.py egg_info failed with error code 1 in /Users/aps/Dropbox/experiments/build/scikit-image
I don't understand this, because from Python, numpy 1.7 is already on my path.
$ python
Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.__version__
'1.7.1'
What is going on - why can't the system installing scikit-image see the newest version of numpy? And how can I fix this?
The path to numpy already seems to be in my ~/.bash_profile:
>>> numpy.__path__
['/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy']
>>> exit()
$ vi ~/.bash_profile
...
export PYTHONPATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages:$PYTHONPATH
UPDATE:
numpy version 1.7 is also in the su path:
$ sudo python
Password:
Python 2.7.5 (default, Aug 1 2013, 00:59:40)
[GCC 4.2.1 Compatible Apple Clang 4.1 ((tags/Apple/clang-421.11.66))] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.__version__
'1.7.1'
You need to make sure that all those packages are available within the virtualenv itself. Did you try running pip freeze after sourcing bin/activate? Using the virtualenv package, the only library that comes "preinstalled" by default is distribute, and all other dependencies must be manually added. With venv (built into py3k) all of your system libraries should be available directly. Which are you using?