I am using Anaconda/Jupyter with Python 2.7. However, I need to upgrade to Python 3. I tried the advice in How to install 2 Anacondas (Python 2.7 and 3.4) on Mac OS 10.9 but that gave me a "Package missing" error, which I could not resolve. Also, on the conda site, they advice that one can do the following:
conda install python=3.5
but this just shows me which specifications are in conflict. There are 8 of them, and it seems like a of work and potential for mishaps to try to resolve all of those, and instead, I would like to remove the current anaconda and do a clean install of it with Python 3.5. But I can't find any information on how to do that.
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I'm relatively new on dealing with python libraries so it might be a stupid question but here is the detailed problem:
I'm working on Linux and trying to use a python program (ORF-rater) using python 3.7. Unfortunately, when I run the program, I get the following error:
ImportError: cannot import name 'maketrans' from 'string'
which I think is related to this issue. Therefore I want to use another version of Python (3.4 or 2.7 for instance) that will support this maketrans.
The program that I'm using also uses the Python package plastid, which I installed using Conda conda install -c bioconda plastid which I guess worked well.
However, it installed the package on python 3.7 only, and I can't find a way to install for python 3.4 (I tried others things as pip3.4 install plastid, but it did not work, most likely because I'm working on an university server and I don't have permission to do it).
In brief, how do I install a package using Conda for a specific version of Python (3.4)?
The following code creates an environment with a specific python version (2.7 since 3.4 was not an option), then you activate it and install the package you need.
conda create -n test python=2.7
conda activate test
conda install -c bioconda plastid
python
Then in Python, I did the following and got no errors
from string import maketrans
I am trying to set and install some packages with python. I have already installed python3 along with Anaconda.
My first question is that when I type:
$ python3
Anaconda says: "$" is not an internal or external command. Should I be using a different command or how can I fix this?
My second question is this: I am trying to install the packages from these four sites based on a book I got:
NumPy: http://docs.scipy.org/doc/numpy-1.10.1/user/install.html
SciPy: http://www.scipy.org/install.html
scikit-learn: http://scikit-learn.org/stable/install.html
matplotlib: http://matplotlib.org/1.4.2/users/installing.html
This note was in there as well: "If you are on Windows, you should have installed a SciPy-stack compatible version of Python 3".
When I go to copy the line for installing the packages on windows and pasting it into my terminal, it gives the error: "The system can not find the file specified"
How can I fix this?
Don't type the $, just python3.
The packages you mention are already included in Anaconda python distribution.
$ is usually used to indicate the start of a line that should be executed in a terminal window. So, therefore, remove the $ and write everything that comes afterwards.
If you installed Anaconda, then you should have the conda command available to you. Besides scikit-learn, the packages should already be installed with your Anaconda distribution. What you could do is $ conda install scikit-learn and this should install scikit-learn for you.
I recommend you to look at the documentation of Anaconda at the Anaconda website (https://docs.anaconda.com/anaconda/) to learn more on how Anaconda, packages and Python works.
Just as emmv said, a few other things in my mind:
You installed Python with Anaconda. I assume you did not add Python to PATH. You should check Anaconda website for any further installments, downloads etc.
Anaconda uses a simple "conda" command, after all. Really, just look at Anaconda's website if you are confused.
please help installing SciPy. I think i've tried almost any advice i could find, but still no luck.
I am using Mac High OS Sierra 10.13.1, python 3.7, trying to make this work for IntellIJ IDEA 2017.2 IDE. I have Xcode version 9.2 if that helps.
I've tried instaling from IDE, using package installer -> fails with error status code 1.
I've tried installing using pip3 install scipy
I've installed brew install gcc ( I have version 7.2.0 installed)
I've installed numpy.
I've tried to install using Macports as suggested on official site - didn't help.
I've tried to instal using brew install scipy.
I've tried to install using Conda. It installed somewhere to Conda Dir, but i still cannot access library from python file using import scipy, error: No module named scipy.
Looks like i am just going in loops now, can some one suggest any idea please?
Topics i researched:
SciPy build/install Mac Osx
Can't install Scipy through pip
"failed with error code 1" while installing scipy
Some other ones i lost links to.
Ok looks like i made it work.
This thread: helped me.
It appeared I was actaully able to install scipy package using conda. But my Python didn't see the package. So i had to:
Change Right Click on my project in IDE > Project > New > Python SDK > Add Local
Select Python in Conda dir. In my case it was /Users/[my user ]/miniconda3/bin/python3.6
Restart IDE just in case and my python script was able to see import scipy.
The downside of this - that I cannot install packages the clean way from IDE anymore for some reason. I.e. Tools > Manage Python Packages > + > doesn't find any. And I have to reinstall all the packages i had using conda install [package name] from terminal . But I am fine with it, as long as it works.
Hopefully my quest might be useful for someone.
The python I use is the one of MacOS. It seems that the python of the system did not carry pip, and pip is installed by myself.
It's very annoying to use the python of the system, there is always the "Permission denied" issue and I'm tired of this. So, I want to uninstall all the packages by pip firstly, and then use virtualenv. Before that, I'd like to know
Is it dangerous if I uninstall all the packages in pip list on MacOS?
Edit: Currently, there are both Python 2.6 and 2.7 on my mac in the directory: /Library/Python. Then can I remove python 2.7 totally and reinstall it in another way?
Do not uninstall MacOS python packages. I did that once. Wasn't a fun time. Even installing new packages can lead to huge problems as dependencies get updated and no longer work with OSX stuff, particularly stuff you can't even update because of SIP.
If you make a virtualenv, it will be totally separate from the OSX python. You can use pip in the virtualenv and it will not effect the pip outside of the virtualenv. In otherwords, you don't need to remove anything - just make the virtualenv and start pip insall'ing :)
I ended up installing Anaconda Python from Continuum Analytics and then setting my path to that python. This way I got an updated python to work with (plus a bunch of other advantages) but my Mac could keep Python 2.6 it needs to operate properly.
I went thought and installed pip and then added a bunch of libraries that I like to use and then, only after installing everything, did I realize that everything went into the 2.7.2 sit-packages directory, so the Python2.7.5 version doesn't see anything.
Now, If I type python --version in the terminal, the correct version is started. However, pip is still "tied" to the default version of Python.
How do I go about telling OSX to look at the new version of Python for everything?
Honestly, one way around this is to make sure that virtualenv works with the right version, and just use pip inside the virtualenv.
A common pattern of Python installation on the mac is to use Home Brew which is a package manager for the mac. You can then install python using:
sudo brew update
brew install python
Provided you have the XCode command line tools already installed.
After I think that the Home Brew Python will be the first in the path. If this is not the case, it might be simpler to use a virtualenv by installing the package with the pip provided by the Mac Brew install (/usr/local/Cellar/python/2.7.5/bin/pip).
After this is done you need to create a virtualenv
virtualenv ~/path/to/the/env
and to activate it
source ~/path/to/the/env/bin/activate
This will be a brand new python and your path will be configured correctly (the python and the pip will be the right ones). You can always delete it, deactivate it or source it as needed.