The Anaconda website states that Over 150 packages are automatically installed with Anaconda. Of which I assume it is referring to the packages with a check mark under "In Installer".
However, it appears that not all packages that are "In Installer" are actually installed
e.g. sympy is stated as "In Installer" however, when I create an environment and firing up python, import sympy gives No module named 'sympy' and I have to run conda install sympy to install it
My question is, how do I interpret the meaning of "automatically installed with Anaconda" and "In Installer"?
The default packages (installed via the installer) are present in the root environment. If you want to have those packages in a newly created environment, simply clone the environment containing those packages:
(root) ~/condaexpts$ conda create -yn sympyenv --clone root
Source: /home/ubuntu/condaexpts/m2
Destination: /home/ubuntu/condaexpts/m2/envs/sympyenv
The following packages cannot be cloned out of the root environment:
- conda-4.3.9-py27_0
- conda-env-2.6.0-0
Packages: 26
Files: 0
#
# To activate this environment, use:
# > source activate sympyenv
#
# To deactivate this environment, use:
# > source deactivate sympyenv
#
(root) ~/condaexpts$ source activate sympyenv
(sympyenv) ubuntu#gitlab:~/condaexpts$ python
Python 2.7.12 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:42:40)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
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 sympy
>>> sympy.__version__
'1.0'
>>>
Related
How can I update xarray? I tried:
>>> import xarray
>>> xarray.show_versions
<function show_versions at 0x7fcfaf2aa820>
But I cannot find any documentation how to read this, or how to update to a new version of xarray.
I was not the person to install it on the computer, so I do not know if it was through anaconda or something else. Is there a way to find this out?
xarray.show_versions is a function, which prints the versions of xarray and its dependencies.
To get just the version of xarray, you can check the __version__ property of the module.
Updating xarray is best done with pip or conda, depending on how you installed it in the first place.
import xarray as xr
print(xr.__version__)
# '0.18.2'
xr.show_versions()
INSTALLED VERSIONS
------------------
commit: None
python: 3.8.8 (default, Feb 19 2021, 18:07:06)
[GCC 8.3.0]
python-bits: 64
OS: Linux
OS-release: 5.11.0-27-generic
machine: x86_64
processor:
byteorder: little
LC_ALL: C.UTF-8
LANG: C.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.0
libnetcdf: 4.7.4
xarray: 0.18.2
pandas: 1.2.4
numpy: 1.20.3
scipy: 1.6.3
netCDF4: 1.5.6
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: 2.8.3
cftime: 1.5.0
nc_time_axis: None
PseudoNetCDF: None
rasterio: 1.2.3
cfgrib: None
iris: None
bottleneck: 1.3.2
dask: 2021.05.0
distributed: 2021.05.0
matplotlib: 3.4.2
cartopy: None
seaborn: None
numbagg: None
pint: None
setuptools: 53.0.0
pip: 21.1.1
conda: None
pytest: None
IPython: 7.23.1
sphinx: None
To update xarray:
pip install --upgrade xarray
or
conda update xarray
To see if it was installed using conda or pip, run conda list xarray. If it was installed using pip, it should state pypi in the Channel column.
This is for those who want to do through GUI and who use software like pycharm, spyder, or other similar softwares.
SO, try finding 'python interpreter' in the settings. Most softwares shows the existing packages, current version,latest version(for example see the image of pycharm)
There is option to select the version that you want. for example there are times, when a module is in its beta phase and is not stable in usage. so, you can specify the latest stable version too. It is applicable for any module and not limited to xarray.
I'm trying to install a module from withing a python script using pip. Here is the contents of script.py:
#/usr/bin/python2.7
# I'm the file called `script.py`
import sys, importlib, pip
print(sys.version); print(sys.path) # For debugging
try:
importlib.import_module('docopt')
except ImportError:
pip.main(['install', '-U', 'docopt'])
finally:
globals()[pack] = importlib.import_module('docopt')
Runnting this script, e.g. using python2.7 script.py gives me:
$ python2.7 script.py
2.7.9 (default, Oct 3 2016, 17:42:24)
[GCC 4.3.2 20081105 (Red Hat 4.3.2-7)]
['/usr/lib/python27.zip', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/lib/python2.7/site-packages']
No module named docopt
Downloading/unpacking docopt
Cannot fetch index base URL https://pypi.python.org/simple/
Could not find any downloads that satisfy the requirement docopt
Cleaning up...
No distributions at all found for docopt
Storing debug log for failure in /root/.pip/pip.log
Traceback (most recent call last):
[...]
File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
ImportError: No module named docopt
So problems with internet connection/ssl or something transport related. However, the same commands work perfectly fine in the python interactive interpreter, when I enter them by hand (copy&paste them):
$ python2.7
Python 2.7.9 (default, Oct 3 2016, 17:42:24)
[GCC 4.3.2 20081105 (Red Hat 4.3.2-7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pip, sys
>>> print(sys.path)
['/usr/lib/python27.zip', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/lib/python2.7/site-packages']
>>> pip.main(['install', '-U', 'docopt'])
Downloading/unpacking docopt
Downloading docopt-0.6.2.tar.gz
Running setup.py (path:/tmp/pip_build_root/docopt/setup.py) egg_info for package docopt
Installing collected packages: docopt
Running setup.py install for docopt
Successfully installed docopt
Cleaning up...
0
Again, the thing that weirds me out is, that it works interactively i.e. running python2.7 in the shell and then entering the very same code by hand. However, not when I run the script file with python2.7 script.py. So In one case, on the same machine, the same interpreter has internet access in the other case it does not.
I'm running out of troubleshooting ideas. I used the same machine and user to get above results. There is no python-startup file, so that is not making the commands magically work interactively. The contents of sys.path are the same in both cases. I'm not behind a proxy. Any ideas what could be missing in the script?
Cannot fetch index base URL https://pypi.python.org/simple/
indicates that for some reason your python interpreter cannot access to internet. There can be plenty of reasons for that. Do you use a HTTP proxy ?
I have recently updated to OSX El Capitain upgrading an exhisting working osx installation. Now I have a module, installed via pip on an anaconda distribution which is now broken. Or better the module can be correctly imported from python
Python 2.7.10 |Anaconda 2.3.0 (x86_64)| (default, Sep 15 2015, 14:29:08)
[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 MDSplus as mds
whereas it does not load on ipython, claiming not to finding a library.
Python 2.7.10 |Anaconda 2.3.0 (x86_64)| (default, Sep 15 2015, 14:29:08)
Type "copyright", "credits" or "license" for more information.
IPython 4.0.0 -- 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.
Using matplotlib backend: MacOSX
In [1]: import MDSplus as mds
Error importing MDSplus package: Error finding library: MdsShr
The library is correctly installed, it is listed in /etc/profile, it is located in /usr/local (so there should not be a problem with the new security system of OSX el Captain) and the python interpreted which is called via python or ipython is the same (Anaconda 2.3.0).
How can I diagnose which is the problem?
EDIT:
the solution proposed in https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/PEuOKEM5fdc does not worked for me. It does not seem to be an environment problem and the command
echo $DYLD_LIBRARY_PATH
points to the correct path
EDIT:
which -a ipython
ipython is /Users/vianello/anaconda/bin/ipython
which -a python
python is /Users/vianello/anaconda/bin/python
python is /usr/bin/python
>>> import sys
>>> for x in sys.path: print x
>>>/Users/vianello/anaconda/lib/python2.7/site-packages/pyhht-0.0.1-py2.7.egg
>>>/Users/vianello/anaconda/lib/python2.7/site-packages/MitDevices-0.3-py2.7.egg
>>>/Users/vianello/anaconda/lib/python2.7/site-packages/MDSplus-alpha_7.0.157-py2.7.egg
>>>//anaconda/lib/python2.7/site-packages/MDSplus-alpha_7.0.147-py2.7.egg/MDSplus
>>>/Users/vianello/anaconda/lib/python27.zip
>>>/Users/vianello/anaconda/lib/python2.7
>>>/Users/vianello/anaconda/lib/python2.7/plat-darwin
>>>/Users/vianello/anaconda/lib/python2.7/plat-mac
>>>/Users/vianello/anaconda/lib/python2.7/plat-mac/lib-scriptpackages
>>>/Users/vianello/anaconda/lib/python2.7/lib-tk
>>>/Users/vianello/anaconda/lib/python2.7/lib-old
>>>/Users/vianello/anaconda/lib/python2.7/lib-dynload
>>>/Users/vianello/anaconda/lib/python2.7/site-packages
>>>/Users/vianello/anaconda/lib/python2.7/site-packages/PIL
>>>/Users/vianello/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg
>>>/Users/vianello/anaconda/lib/python2.7/site-packages/aeosa
>>>/Users/vianello/anaconda/lib/python2.7/site-packages/lmfit-0.8.3-py2.7.egg
>>>/Users/vianello/anaconda/lib/python2.7/site-packages/setuptools-18.3.2-py2.7.egg
>>>/Users/vianello/anaconda/lib/python2.7/site-packages/suds-0.4-py2.7.egg
in iPython the same give the results
/Users/vianello/anaconda/bin
/Users/vianello/anaconda/lib/python2.7/site-packages/pyhht-0.0.1-py2.7.egg
/Users/vianello/anaconda/lib/python2.7/site-packages/MitDevices-0.3-py2.7.egg
/Users/vianello/anaconda/lib/python2.7/site-packages/MDSplus-alpha_7.0.157-py2.7.egg
/Users/vianello/anaconda/lib/python27.zip
/Users/vianello/anaconda/lib/python2.7
/Users/vianello/anaconda/lib/python2.7/plat-darwin
/Users/vianello/anaconda/lib/python2.7/plat-mac
/Users/vianello/anaconda/lib/python2.7/plat-mac/lib-scriptpackages
/Users/vianello/anaconda/lib/python2.7/lib-tk
/Users/vianello/anaconda/lib/python2.7/lib-old
/Users/vianello/anaconda/lib/python2.7/lib-dynload
/Users/vianello/anaconda/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg
/Users/vianello/anaconda/lib/python2.7/site-packages/lmfit-0.8.3-py2.7.egg
/Users/vianello/anaconda/lib/python2.7/site-packages/setuptools-18.3.2-py2.7.egg
/Users/vianello/anaconda/lib/python2.7/site-packages/suds-0.4-py2.7.egg
/Users/vianello/anaconda/lib/python2.7/site-packages
/Users/vianello/anaconda/lib/python2.7/site-packages/PIL
/Users/vianello/anaconda/lib/python2.7/site-packages/aeosa
/Users/vianello/anaconda/lib/python2.7/site-packages/IPython/extensions
/Users/vianello/.ipython
Thus the MDSplus-alpha_7.0.157-py2.7.egg can be seen both from python and ipython
My first thought is that you are running afoul of the new Apple System Integrity Protection. iPython is launched using a shell script that loads via /bin/bash. That will result in your DYLD_LIBRARY_PATH environment variable being stripped when python launches. You can check this by importing os and then attempting to print the contents of os.environ["DYLD_LIBRARY_PATH"]. If that print throws an exception then you know what the problem is.
A simple fix that works for me is to edit the first line of the ipython script so that the #! calls your python binary directly rather than going via bash. This is not a long term solution as it will have to be redone each time ipython is updated until upstream changes (to be fair I'm not sure why bash is involved).
I have written a report on python and library paths at http://dmtn-001.lsst.io
How do I make all modules be available for both python 2.7 and 3.4?
I executed:
$ brew install <prerequisites for pygame>
<snip snip>
<snip snip>
$ brew install pygame
$ pip freeze
<snip snip>
pygame==1.9.2a0
<snip snip>
and can see pygame is installed. When I open a new shell/terminal and run python 2.7 and type import pygame, I have no problems:
Python 2.7.9 |Anaconda 2.2.0 (x86_64)| (default, Dec 15 2014, 10:37:34)
[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://binstar.org
>>> import pygame
>>>
However, when I run python 3.4 and type import pygame, it says there's no module named pygame.
/usr/local/bin/python3
Python 3.4.2 (default, Dec 11 2014, 17:48:01)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pygame
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named 'pygame'
>>>
What do I need to do to make 3.4 see/link with all the modules that 2.7 sees?
P.S. I don't know how but pip is running from anaconda, which I think I might have installed when installing numpy or panda or something.
You cannot use modules installed for Python 2 in Python 3. Python 2 and Python 3 are not compatible, that is why most libraries offer a Python 2 and a Python 3 version.
So if you have PyGame installed with pip2, you can only use it with Python 2. To use PyGame in Python 3, you need to install it with pip3. Afterwards you will have both versions on your computer, so that a project that uses your Python 2 interpreter uses the PyGame installed by pip2 and a project that uses Python 3 interpreter uses the pyGame installed by pip3.
Example:
# test.py
import pygame
In the console:
> python3 test.py # imports pygame from /usr/lib/Python3.x/site-packages
> python2 test.py # imports pygame from /usr/lib/Python2.x/site-packages
You should not use Python 2 modules with Python 3 (and vice versa). Instead, install those separately, e.g.
pip3 install pygame
Sometimes, the code bases for a package will be compatible between 2 and 3, but quite often, they are not (especially when shared object modules, *.so files, come into play).
Also, Python 2 will not have the Python 3 packages library in sys.path by default, and vice versa. For a good reason.
All in all, consider Python 2 and Python 3 two different languages, for which you have to do everything separately. They just happen to be very much alike.
(Personal opinion/bit of advocacy: use and write your code in Python 3, unless you have a very good reason no to (unported essential libraries, chance of losing your job). It's relatively straightforward in 99% of the cases to make it Python 2 compatible later on, if really needed.)
I've installed Python 2.7 and python 3.4 on my system. Earlier i was using 3.4 but now require 2.7 as well (for a course I'm taking, which requires some files which are not there for 3.4). When I type python in cmd it by default initializes 3.4. Is there some way to change it to 2.7 by default?
Thanks
UPDATE: I was able to invoke it using 'py'. Here's the link if anyone else has a confusion. https://docs.python.org/3/using/windows.html?highlight=shebang#python-launcher-for-windows (from some other answer)
Update:
If your system environment is Windows:
1) call py -2.7 or py -3 based on the version you want.
2) change your PATH system environment variable , makes sure it refers to the version you want.
You can do it in serveral ways on Linux environment:
1)
call a specific Python binary you can call the explicit full path (e. g. /usr/local/bin/python). This will call the same executable regardless of the value of the $PATH variable.
2)
configure your accounts so that both have the same binary first in the $PATH variable.
3)
call python2 and python3; many installations symlink these to the corresponding binaries.
$ python2
Python 2.7.6 (default, Mar 22 2014, 22:59:56)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>
$ python3
Python 3.4.0 (default, Apr 11 2014, 13:05:11)
[GCC 4.8.2] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>