Python numpy update from 1.6 to 1.8 - python

I have installed numpy 1.8. But when I do print numpy.__version__ it says 1.6.
What do I have to change to get python to realize where numpy is? Working on a Mac (10.9). I'm using python 2.7.6.
Edit:
I've tried to delete all my versions of numpy. I did pip uninstall numpy. And then I typed:
python
import numpy
print numpy.version
and it printed out 1.6.2
I can't delete numpy apparently.


I am running Python 2.7.5 on Mac OS X 10.9.4, and this appears to be some kind of weird bug in how the Macintosh factory-installed version of Python is handling upgraded package installations.
In my case, when I do:
sudo pip uninstall numpy
it removes the version of numpy installed under
/Library/Python/2.7/site-packages
However, this does not mean that numpy is fully removed from the system! There are a second set of "backup" versions of several Python packages installed also at:
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python
When I install numpy using the /usr/bin/easy_install utility that Apple shipped with the OS X system, the latest version (currently at 1.9.0, as of this posting) of numpy is loaded into Library/Python/2.7/site-packages, just as one would expect, and it correctly precedes the "OS X system default" version of numpy in the module load path so that the latest version of numpy is loaded when I do import numpy in Python. However--and this is the really weird, apparently buggy behavior!--when I uninstall numpy, and instead reinstall using either pip, or by doing:
sudo python setup.py install
on a .tar.gz distribution downloaded directly from sourceforge, the upgraded installation does not appear to take precedence in the Python module load path, even though it is also installed under /Library/Python/2.7/site-packages!
Anyway, to fix the problem (or rather, I should probably say, to work around the bug, at least on Max OS X), follow this procedure:
Uninstall the numpy package from /Library/Python/2.7/site-packages using the method of your choice (pip uninstall numpy appeared to work for me)
Verify that there is indeed no longer any numpy package still remaining under /Library/Python/2.7/site-packages
Reinstall numpy using the factory-included /usr/bin/easy_install. Do not use any other alternative method, at least not if you want to use numpy with the Apple factory-installed version of Python 2.7
Alternatively, using a completely different distribution of Python (e.g., Canopy or Anaconda), as one of the other commenters already mentioned, should also work as well.


You mentioned in the comments that removing with pip and OS package manager didn't work for you. If you may have used easy_install in the first place, also try easy_install -m for removal. If all else fails, you can clobber the files manually (the imports are taken from sys.path so the first version found in that list is where the import will come from).
Load up interactive python interpreter and check the physical location of the files:
>>> import numpy
>>> numpy.__file__
'/home/wim/.virtualenvs/xyz/local/lib/python2.7/site-packages/numpy/__init__.pyc'
This will tell you which directory you need to delete in order to prevent the unwanted version from being imported.
This is a somewhat impolite way to "uninstall" numpy, so use as a last resort.


I assume you have inconsistent version of numpy in two paths
/Library/Python/2.7/site-packages
and
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python
My solution is rename (or delete) the one you don't like (possibly the older version) and symlink the other (the newer version) back to the directory which you deleted numpy folder from.

Related

I have installed Numpy but PyCharm can't find the module

When I run import numpy as np
I get ModuleNotFoundError: No module named 'numpy'
I have tried it in the project I always used, I have tried it in a new project where Conda is the environment used but I always get this error. I am clueless here.
When I type in the Terminal of my Macbook pip3 install numpy I get the answer that I already have numpy Requirement already satisfied: numpy in /opt/anaconda3/lib/python3.9/site-packages (1.21.5)

Often, many IDEs (like Spyder, Jupyter Notebook, or PyCharm) installs their own virtual environment of python to keep things easy and simple for them from your global python.
even if you have a package installed in your global python, you might not able to use it in your virtual environment since it would have separate package management.
So the solution is to install the package using the IDEs.
In your case you can do it by using their terminal or using the red bulb (which will appear on the top of your pakage)

Update Python to 3.8 and the modules doesn't work

I had Python3.5.2 installed on /usr/bin/.
All the modules include scipy and numpy works well.
But, after I installed Python3.8 the modules scipy and numpy doesn't work.
I saw that Python3.8 is in usr/local/bin instead usr/bin.
So, how can I run Python3.8 using all the modules like I used with Python3.5.2?

Python 3.8.0 was just released on 2019-10-14, so several modules are not yet supported (as of 2019-10-31). SciPy, Matplotlib, and SciKit-Learn are not yet supported. These may be supported by the time 3.8.1 is released in 2019-12-16.
Numpy and Pandas are supported, but for the others you will need to continue using a supported version of Python. To keep both versions on your machine, I would recommend using a virtual environment.

How to find and uninstall the numpy duplicate versions

I am trying to install the library GPy. Although the installation is successful, I have a question on my numpy version.
GPy library can be found here https://github.com/SheffieldML/GPy
The current version of my numpy is 1.9.3
>>> import numpy
>>> numpy.version.version
'1.9.3'
But when I perform python setup.py install for GPy, it refers to numpy 1.10.0. I checked in python 2.7/site-packages there only one version of numpy exist that too 1.9.3
Using /home/vinod/anaconda/lib/python2.7/site-packages
Searching for scipy==0.16.0
Best match: scipy 0.16.0
Adding scipy 0.16.0 to easy-install.pth file
Using /home/vinod/anaconda/lib/python2.7/site-packages
Searching for numpy==1.10.0
Best match: numpy 1.10.0
Adding numpy 1.10.0 to easy-install.pth file
Using /home/vinod/anaconda/lib/python2.7/site-packages
Finished processing dependencies for GPy==0.8.8
vinod#vinod-Lenovo-G580:~/GPy$
Since it's referring to another version am getting error like
File"__init__.pxd", line 155, in init GPy.util.linalg_cython (GPy/util/linalg_cython.c:4238)
ValueError: numpy.dtype has the wrong size, try recompiling
Could anyone tell me how to find and remove the numpy 1.10.0 ?

From the conda FAQ:
conda update numpy --no-pin

I tried the following steps and it works but still I don't know how.
I opened the setup.py and changed the numpy condition from numpy >= 1.7 to numpy <=1.9.3
Then I performed the python setup.py install
Then I uninstalled GPy using pip uninstall GPy
Again I installed GPy but using pip install GPy. Note: in previous steps I used git and installed separately.
This time it upgraded my numpy to 1.10.0 during installation and got installed successfully
Finally now it works well.

python Packeges
installed
select the library you want to unistall
"delate" by selecting tenter image description herehe menu on the right

Matplotlib won't install properly on Python 3.5

I've just installed Python 3.5 to experience its functionality. The problem is that all the modules I use in my daily programming have been installed and run very well on it except Matplotlib. I installed it via pip and never faced any errors while installing, but when I wanted to import it, the error saying, DLL load failed: The specified module could not be found. popped up.
What's the matter with Python 3.5, or Matplotlib?

Uninstall the module using pip uninstall matplotlib then install it again using http://matplotlib.org/downloads.html
Obtain the .exe file that best fits your machine, in my case it would be matplotlib-1.4.3.win-amd64-py3.4.exe. This will be a more complete version of matplotlib for windows rather than using pip.
I would also consider rolling back to Python 3.4 unless you absolutely need 3.5. There shouldn't be a compatibility issue between 3.4 and 3.5 for Python, but as far as matplotlib it's been tested with 3.4, but if you run through problems on 3.5 I would roll back.

If you have Python 3.5 you should install MS's Redistributable DLLs to make matplotlib working on Windows... In my case, no need to reinstall matplotlib even...
Try this example without. If error appears install that and try with it (you must log in MS site and download version for arch you using - i tested x86 only, Windows 7, Python 3.5).
That case is included in matplotlib install documentation!
Remember, you should always read documentation before you ask!

ValueError: numpy.dtype has the wrong size, try recompiling

I just installed pandas and statsmodels package on my python 2.7
When I tried "import pandas as pd", this error message comes out.
Can anyone help? Thanks!!!
numpy.dtype has the wrong size, try recompiling
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\analytics\ext\python27\lib\site-packages\statsmodels-0.5.0-py2.7-win32.egg\statsmodels\formula\__init__.py",
line 4, in <module>
from formulatools import handle_formula_data
File "C:\analytics\ext\python27\lib\site-packages\statsmodels-0.5.0-py2.7-win32.egg\statsmodels\formula\formulatools.p
y", line 1, in <module>
import statsmodels.tools.data as data_util
File "C:\analytics\ext\python27\lib\site-packages\statsmodels-0.5.0-py2.7-win32.egg\statsmodels\tools\__init__.py", li
ne 1, in <module>
from tools import add_constant, categorical
File "C:\analytics\ext\python27\lib\site-packages\statsmodels-0.5.0-py2.7-win32.egg\statsmodels\tools\tools.py", line
14, in <module>
from pandas import DataFrame
File "C:\analytics\ext\python27\lib\site-packages\pandas\__init__.py", line 6, in <module>
from . import hashtable, tslib, lib
File "numpy.pxd", line 157, in init pandas.tslib (pandas\tslib.c:49133)
ValueError: numpy.dtype has the wrong size, try recompiling

(to expand a bit on my comment)
Numpy developers follow in general a policy of keeping a backward compatible binary interface (ABI). However, the ABI is not forward compatible.
What that means:
A package, that uses numpy in a compiled extension, is compiled against a specific version of numpy. Future version of numpy will be compatible with the compiled extension of the package (for exception see below).
Distributers of those other packages do not need to recompile their package against a newer versions of numpy and users do not need to update these other packages, when users update to a newer version of numpy.
However, this does not go in the other direction. If a package is compiled against a specific numpy version, say 1.7, then there is no guarantee that the binaries of that package will work with older numpy versions, say 1.6, and very often or most of the time they will not.
The binary distribution of packages like pandas and statsmodels, that are compiled against a recent version of numpy, will not work when an older version of numpy is installed.
Some packages, for example matplotlib, if I remember correctly, compile their extensions against the oldest numpy version that they support. In this case, users with the same old or any more recent version of numpy can use those binaries.
The error message in the question is a typical result of binary incompatibilities.
The solution is to get a binary compatible version, either by updating numpy to at least the version against which pandas or statsmodels were compiled, or to recompile pandas and statsmodels against the older version of numpy that is already installed.
Breaking the ABI backward compatibility:
Sometimes improvements or refactorings in numpy break ABI backward compatibility. This happened (unintentionally) with numpy 1.4.0.
As a consequence, users that updated numpy to 1.4.0, had binary incompatibilities with all other compiled packages, that were compiled against a previous version of numpy. This requires that all packages with binary extensions that use numpy have to be recompiled to work with the ABI incompatible version.

For me (Mac OS X Maverics, Python 2.7)
easy_install --upgrade numpy
helped. After this you can install up-to-date packages pandas, scikit-learn, e.t.c. using pip:
pip install pandas

I found it to be a simple version being outdated or mismatch and was fixed with:
pip install --upgrade numpy
pip install --upgrade scipy
pip install --upgrade pandas
Or might work with the one liner:
pip install --upgrade numpy scipy pandas

I had a similar error with another library and realized that I had several versions of numpy installed on my system. The fix for me was to edit my PYTHONPATH and put the site-packages that contained the latest version of numpy in first position.

As in here, for me only sudo pip install pandas==0.13.1 worked

I also encounter this error when use pandas to access MYSQL.
This error message indicates a binary compatible issue and can be resolved by
using latest version of pandas and numpy package.
Here is my steps to resolve this issue, and it works well on my Ubuntu 12.04:
cd /tmp/
wget https://pypi.python.org/packages/source/p/pandas/pandas-0.12.0.tar.gz
tar xzvf pandas-0.12.0.tar.gz
cd pandas-0.12.0
easy_install --upgrade numpy

In my case, I had installed pandas-0.10.0.win-amd64-py2.7 but was checking to see if a bug had been fixed in a more recent version of pandas. So I did an easy_install -U to force the upgrade, but then got the above error due to some incompatibilities with numpy etc... when I did
import pandas
To fix, I just reinstalled the pandas-0.10.0.win-amd64-py2.7 binary and everything works. I didn't see this answer (suggests to use pip) which may have helped me (though not sure) Install particular version with easy_install
Also this highlights why one should use virtualenv (which I wasn't).

For me (Mac OS X Mavericks) it worked to install the version for python2.6:
sudo port install py26-scikit-learn
then run:
python2.6 myscript.py

The problem I solved on Webfaction was old numpy library(1.5) which was in conflict with my fresh
pip install pandas
installation in .virtualenv.
The problem was solved after I did pip install pandas out of the virtual environment.
The idea came from discussion on https://github.com/pydata/pandas/issues/3711, thanks, cpcloud!

I just meet this 'ValueError' issue and have addressed it. Definitely there's something wrong with numpy package.
But when I try to pip install --upgrade numpy it failed, so I uninstall and download the newest numpy.zip file.
Then manually uncompress and python setup.py install it.
Luckly, it works!

Like #user333700 said, required versions of libraries may not meet for each other. You get one library as another's dependency. Then without knowing it was already installed as dependency, you need that specific library and you install one version. With such ways dependencies may mess up.
I lived such a case and looked for a solution. Found this:
https://stackoverflow.com/a/12975518/1694344
I had two different versions for egg-info file and folder name of numpy:
drwxr-xr-x. 19 root root 4096 Sep 25 15:00 numpy
drwxr-xr-x. 2 root root 4096 Sep 22 11:25 numpy-1.13.1.dist-info
-rw-r--r--. 1 root root 1630 Nov 20 2015 numpy-1.7.1-py2.7.egg-info
I removed them all and reinstalled numpy with pip.

I had a similar issue, and simply re-installing using pip install ... as suggested in previous comments didn't work.
What worked for me was re-installing with the added flag pip install --no-cache-dir ..., seems there was an incompatible numpy version somewhere in the cache.

There are cases where you want to keep a specific NumPy version and the upgrade option mentioned here will not work.
An example that occurred to me was the Python distribution preinstalled with ArcGIS. For ArcPy to work in ArcGIS 10.5.1, that distribution needs to be Python 2.7.12 with NumPy 1.9.3 and any other version of NumPy is probably going to cause issues with your ArcPy functionality.
What you can do with this case is try to install a specific, older version of the problematic third-party library that is supposed to be compatible with the older NumPy version that ArcGIS has.
For instance, scikit-learn 0.19.1 would NOT operate with NumPy 1.9.3 and would result in the same error you mentioned. However, scikit-learn 0.15 works fine. You can test different versions to find the one that works. Just mention the version number through pip:
python -m pip install scikit-learn==0.15

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