For work-related reasons, I'm trying to install Python 2.7.8 directly onto my machine (Mac OSX 10.9).
I am current running Python 2.7.6 in Enthought Canopy, and I really don't want to touch the existing libraries there.
My problem is that I'd like to use pip to install packages for the new instantiation of Python, but currently pip is bundled up with Enthought Canopy, so it only installs packages in the site-packages path for Enthought Canopy.
I first tried the following:
pip install --install-option="--prefix=$PREFIX_PATH/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages" scikit-learn
But got the following error:
Requirement already satisfied (use --upgrade to upgrade): scikit-learn in ./Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages
Then, I tried to add the existing Enthought folder to the path for the newly installed Python 2.7.8, By entering the following line at the end of the .bash_profile:
PYTHONPATH=$PYTHONPATH:Users/***/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
This led to errors when trying to import some of the packages, probably for this reason:
Cannot import Scikit-Learn
I would really prefer just to install a new version of scikit-learn in a separate folder. Anyone have any suggestions?
You can use virtualenv to create a self-contained python environment that can be configured and used separately from your regular python installation.
Create the virtualenv (for oldish versions of virtualenv you'd want to include --no-site-packages right after virtualenv):
$ virtualenv limitedenv
Using base prefix '/usr/local/Cellar/python3/3.3.3/Frameworks/Python.framework/Versions/3.3'
New python executable in limitedenv/bin/python3
Also creating executable in limitedenv/bin/python
Installing setuptools, pip...done.
Move into the virtualenv and activate it:
$ cd limitedenv/
$ source bin/activate
(limitedenv)$
Install the packages you're after with pip as you'd do globally:
(limitedenv)$ pip install scikit-learn
Downloading/unpacking scikit-learn
Downloading scikit-learn-0.15.0.tar.gz (7.0MB): ...
scikit-learn will now be installed just inside limitedenv, and as long as you have that environment active, invoking python or pip will be like this is your very own, secluded Python installation.
You can exit from the virtual environment by calling deactivate:
(limitedenv)$ deactivate
$
This allows you to have different versions of python by themselves, different versions of libraries pr. project and different configurations based on what your project requires. virtualenv is a very useful tool!
Related
I have the following version of python
import sys
print(sys.version)
3.6.5 | packaged by conda-forge | (default, Apr 6 2018, 13:44:09)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)]
I installed a package with the following command
pip install wfdb
It is succesfully installed because when I then write the command:
pip show wfdb
The following information appears
Location:
/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages
However, when I type the command import wfdb in Python notebook or the version of python in terminal, I get the following message
No module named 'wfdb'
Does it have to do with the path on which python is checking where the packages are? How to check this and how to change it?
You have (at least) 2 Python installations, one managed by Anaconda, the other what appears to be an official Python.org Mac build installed system-wide. The pip command on the command-line is the one tied to the Python.org Mac build.
pip is a script that is tied to a specific Python installation, and there can be multiple versions of the script installed in different locations, and is usually also installed with pipX and pipX.Y to match the X.Y version indicator of the Python version it is tied to. For Python 3.6, that means the same script would also be available as pip3 and pip3.6. (This also means that pip can be connected to Python 2 or Python 3, depending on your exact OS setup. It is not a given that pip, without a version number, installs into Python 2.x as some answers may claim).
Note that when you run a command without a path in your shell, (such as pip as opposed to /usr/bin/pip), you are asking your shell to find the command for you in a number of locations, listed in the PATH environment variable. The first location in the PATH list with that command is then fixed. which -a <command> would tell you all possible PATH-registered locations that the command can be found in. You can always use the full path to a command to bypass the PATH search path.
You can always verify what Python version the pip command is connected to with:
pip -V
which will output the version of pip and the location it is installed with. It'll print something like
pip pipX.pipY path/to/pythonX.Y/site-packages/pip (python X.Y)
where pipX.pipY is the pip version number and path/to/pythonX.Y tells you what Python installation this is for.
You can try to match this with the Python version by running
python -m site
which outputs the Python module search path for that Python version. Python can be run with python, pythonX and pythonX.Y too, and is subject to the same PATH search.
Note the -m switch there, that instructs Python to find a module in it's module search path and execute it as a script. Loads of modules support being run that way, including pip. This is important as that helps avoid having to search for a better pip command if you already can start the right Python version.
You have several good options here:
Since you are using Anaconda, you could look for a conda package for the same project. There is such a package for wfdb. Install it with
conda install wfdb
Anaconda aims to give you a wider software management experience that includes a broader set of software options than just the Python PyPI ecosystem, and conda packages usually manage more things than just the Python package.
Conda packages are usually maintained by a different set of developers from the package itself, so there may be a newer version available on PyPI (requiring pip install) than there is on Conda.
This is not an option for all Python packages, if there is no conda package you have to use pip. See Installing non-conda packages.
you can use the conda command to create a conda environment. Once you have an environment created, you can activate it with
source activate <name_of_cenv>
to alter your PATH settings. With the envirnoment 'active' the first directory listed on your PATH is the one for the conda environment and the pip command will be the one tied to that environment.
Note that a conda environment gives you an isolated environment for a specific project, keeping the library installation separate from the rest of your Python packages in the central site-packages location. If you want to install a package for all of your Anaconda Python projects, don't use a conda environment.
Use the Anaconda Python binary to run pip as a module; when you can run /path/to/python or pythoncommand to open the right Python version, you can use that same path to run /path/to/python -m pip ... instead of pip ... to be absolutely certain you are installing into the correct Python version.
Look for a better pip command, with which -a pip or which -a pip3.6, etc. But if you already know the Python binary, look in the same bin location for pip. If you have anaconda/bin/python, then there probably is a anaconda/bin/pip too.
As you can read here:
pip3 and pip would make a difference only when you are not using any
environment managers like virualenv (or) conda. Now as you are
creating a conda environment which has python==3.x, pip would be
equivalent to pip3.
For this reason it could be you did not activate your Conda environment before installing required packages and running your code.
Activate the new environment:
On Windows:
activate myenv
On macOS (this should be your option) and Linux:
source activate myenv
NOTE: Replace myenv with the name of the environment.
which python
gives the you the PATH to python
and then /path/to/python -m pip install thepackagetobeinstalled
Many thanks #MartijnPieters
You have installed python2.x package and you're using python3.x. Try:
pip3 install wfdb
If you don't have pip3 run:
[apt-get/yum] install python3-pip
You can see what packages you have currently installed by running:
pip freeze
and for python 3.x packages
pip3 freeze
Please remember each time you install a Python package, it will be placed in the directory for one particular Python version. Hence your error.
I'm trying to teach myself python, and I feel out of my depth. To start, I am working on a mac which already comes with python 2.7 installed.
I installed python 3.6 recently and have been using it to teach myself the basics. I'd like to eventually learn how to produce mathematical plots in python, and I know I will need the matplotlib package to do that.
Following some advice online, I was told that python3 already comes with pip installed, which is what I thought I should use to install matplotlib. The advice said I should type the following into the mac terminal:
python3.6 -m pip install matplotlib
I typed this, and it seemed like the package was installing, but I ended up getting some sort of error code that said:
Command "python setup.py egg_info" failed with error code 1 in [folder].
I tried opening IDLE and typing "import matplotlib", but I got the error: "no module named matplotlib". I also tried typing "import matplotlib.pyplot as plt", but I got the same error.
Based on further research and this youtube video, I've decided to just install miniconda in order to have access to the matplotlib package.
The problem is, I'm not sure if I should somehow be uninstalling whatever was installed when I ran the code above to install matplotlib. I've actually run that line of code 3 or 4 times. Should I remove anything before installing miniconda? Also, I am running python 3.6, while miniconda is listed on the website as being for python 3.5. Does this mean it won't work for my version of python?
Running pip like that would install packages system-wide. I'm guessing it's failing because you're not running as root (i.e. the administrator user). But wait! Don't try again as root! Instead of installing packages, do it in a virtual environment. First create it:
virtualenv myenv
This creates a directory called myenv with a bunch of stuff in it (so make note of where you run this command). Whenever you want to use the virtual environment (like straight away!) you first need to activate it:
. myenv/bin/activate
Don't miss out that dot (followed by a space) at the beginning! As the other answer says, the first thing you should do in it is upgrade pip:
pip install --upgrade pip
Now you're ready install whatever else you like:
pip install matplotlib
One last note: The virtual environment is tied to a particular Python version. By default it uses the system's Python 2.7 installation, so to use a different one you need to specify it when you create the virtual environment, like this (if that Python version is installed system-wide):
virtualenv -p python3.5 myenv
Or like this (if that Python version is not installed system-wide):
virtualenv -p /path/to/my/installation/of/python3.5 myenv
While the virtual environment is activated, you don't need to specify the particular path/version of Python. Just run it like this:
python
I also encountered many problems during my installation.
It seems that version 2 of matplotlib is not compatible with Python version 3.
Finally, I succeeded by specifying version 3 of matplotlib as follows with the following command:
sudo apt-get install python3-matplotlib
Reference from the Matplotlib website:
https://matplotlib.org/users/installing.html#building-on-linux
Try upgrade setup tools
--upgrade setuptools
or
easy_install -U setuptools
or upgrade pip
pip install --upgrade pip
I ended up downloading anaconda and using the python interpreter that comes with it, as anaconda comes with matplotlib and many other python packages of interest.
the pip command typically is for the Python 2. use pip3 instead to install the libraries in the python 3.X path
This should work
pip3 install matplotlib
The solution that work for me in python 3.6 is the following
py -m pip install matplotlib
Matplotlib files are downloaded in ~/.local/lib/python3.6/site-packages/ and not in /usr/lib/python3.6/ .
Try the command:
sudo cp -r ~/.local/lib/python3.6/site-packages/* /usr/lib/python3.6/
I have a MacBook Pro that came pre-installed with python2.7. I later installed python3 and ipython notebook. I installed pip too to install packages, and am able to install packages and run program from python3. However, for another project I need to run code in python2.7, and I am not sure how to install it in python2.7 folder.
I tried using pip for installing packages to 2.7, but it kept giving error saying package already exists. When I check for version of python using --version, I see 2 pythons installed. However, when I check for pip and pip3, both seem to be in th same folder.
Any tips on how to install packages in python2.7, without making any changes to 3.3? I am using python3 and ipython notebooks for another project.
viveks-mbp:~ vivekyadav$ which pip
/Library/Frameworks/Python.framework/Versions/3.3/bin/pip
viveks-mbp:~ vivekyadav$ which pip3
/Library/Frameworks/Python.framework/Versions/3.3/bin/pip3
viveks-mbp:~ vivekyadav$ which python
/usr/bin/python
viveks-mbp:~ vivekyadav$ which python3
/Library/Frameworks/Python.framework/Versions/3.3/bin/python3
You can use the virtualenv to create a kind of sandbox.
$ virtualenv <work-directory>
$ source <work-directory>/bin/activate
The last command initiate your virtual environment, totally isolated from the system. So every pip command will install the package inside this directory.
But you have to run your application inside the virtual environment too.
I am using the Anaconda python distribution on a Mac. I would like to play with the latest version of the matplotlib source code on Github, make a few changes, and see how it runs. But most of the time I would simply like to use the normal version of matplotlib that comes with Anaconda Python, so I would like a way to switch back and forth easily.
The matplotlib documentation has a good description of the branching and pull-request workflow, but it's not clear to me how I actually install and use the development version of matplotlib in a way that will preserve my working Python implementation.
My guess is that I want to set up an environment that contains the latest matplotlib version and it's dependencies and switch between that environment and the normal root environment. But when I use python setup.py develop to install the development version of matplotlib, it seems to install to both environments.
So, what is the best practice for working with the development version of a Python package from GitHub?
As you mentioned in your question, conda env is capable of maintaining separate Python environments for development versions of whichever packages you want to work on.
I'm not quite sure why you are finding that python setup.py develop is installing the dev version of matplotlib to your root environment.
Perhaps you created a new environment, but didn't activate it before installing the dev version of matplotlib? For example:
~$ conda create --name matplotlib-dev --clone root
Fetching package metadata: ....
src_prefix: '/home/alistair/anaconda'
dst_prefix: '/home/alistair/anaconda/envs/matplotlib-dev'
Packages: 165
Files: 32
Linking packages ...
[ COMPLETE ]|#####################################################| 100%
#
# To activate this environment, use:
# $ source activate matplotlib-dev
#
# To deactivate this environment, use:
# $ source deactivate
#
~$ conda info --envs
# conda environments:
#
matplotlib-dev /home/alistair/anaconda/envs/matplotlib-dev
root * /home/alistair/anaconda
At this point I have created a matplotlib-dev environment but I haven't activated it yet, so installing any new packages would still modify my root environment.
~$ source activate matplotlib-dev
discarding /home/alistair/anaconda/bin from PATH
prepending /home/alistair/anaconda/envs/matplotlib-dev/bin to PATH
(matplotlib-dev)~$ conda info --envs
# conda environments:
#
matplotlib-dev * /home/alistair/anaconda/envs/matplotlib-dev
root /home/alistair/anaconda
In any case, using setuptools directly (i.e. python setup.py install or python setup.py develop) is no longer recommended, and might not be supported by future versions of numpy etc..
The preferred method is to use pip install <path>, or pip install -e <path> if you want an "editable" installation (similar to what python setup.py develop gives you):
(matplotlib-dev)~$ pip install -e git+git://github.com/matplotlib/matplotlib.git#egg=matplotlib-dev
Obtaining matplotlib from git+git://github.com/matplotlib/matplotlib.git#egg=matplotlib-dev
Cloning git://github.com/matplotlib/matplotlib.git to ./src/matplotlib
...
Installing collected packages: matplotlib
Running setup.py develop for matplotlib
Successfully installed matplotlib-1.5.0+337.g595868a
(matplotlib-dev)~$ python -c "import matplotlib; print(matplotlib.__version__)"
1.5.0.post337+g595868a
(matplotlib-dev)~$ source deactivate
discarding /home/alistair/anaconda/envs/matplotlib-dev/bin from PATH
~$ python -c "import matplotlib; print(matplotlib.__version__)"
1.4.3
Note the #egg= part, which tells pip to install the source to ./src/matplotlib-dev. Instead of a git URI you could also pass pip the path to a local source directory if you've already got a local copy that you're currently working on.
It should also be possible to use conda develop <path> instead of pip install -e <path>, although conda doesn't seem to offer integrated VCS support like pip does.
i have installed many python modules plugins and libraries in my centos system.
Now i don't want to install each thing again on separate computers.
Is there any way i can make the package like rpm or any other thing so that when i install in in new location all the modules, dependencies also gets installed and everytime i install new thing i can update the install package
If you have installed the packages with pip (an improved easy_install), you can just do pip freeze > my-reqs.txt to get a list and versions of the installed packages. There is also some option to install using the reqs file, which I can not remember right now.
Pip is meant to companion virtualenv, which can be used to handle per project requirements of dependent packages.
If you are not using Pip, then you should check what packages you have in your global and/or user site-packages directories.
The solutions below are from:
How do I find the location of my Python site-packages directory?
Global site packages:
python -m site
or more concisely:
python -c "import site; print(site.getsitepackages())"
User site packages:
python -m site --user-site
The latter do not however show the site-packages of the current virtual environment – use distutils.sysconfig.get_python_lib() for that:
python -c "from distutils.sysconfig import get_python_lib;
print get_python_lib()"
Note!
You can not just copy over the packages that have C++-extensions or other compiled binaries in them. These have to be reinstalled on other machines.