conda command not found. The .profile and "echo $PATH" seem however okay - python

I've blindly installed numerous times Python, admittedly without fully knowing what I was installing and where. I figured that now before I encounter even more problems that I need to tidy up my environment a bit. In Terminal, I used the command which -a python and came up with this:
/opt/local/bin/python
/Library/Frameworks/Python.framework/Versions/2.7/bin/python
~/anaconda/bin/python
/opt/local/bin/python
/opt/local/bin/python
/opt/local/bin/python
/usr/bin/python
My .profile has:
export PATH="/opt/local/bin:/opt/local/sbin:$PATH"
export PATH="/opt/local/bin:/opt/local/sbin:/opt/local/lib/gmt4/bin:$PATH"
export PATH="~/teqc:$PATH"
export PATH="/usr/local/runpkr000:$PATH"
# Finished adapting your PATH environment variable for use with MacPorts.
##
# Your previous ~/.profile file was backed up as ~/.profile.macports-saved_2015-04-02_at_16:40:23
##
# MacPorts Installer addition on 2015-04-02_at_16:40:23: adding an appropriate
PATH variable for use with MacPorts.
export PATH="/opt/local/bin:/opt/local/sbin:$PATH"
# Finished adapting your PATH environment variable for use with MacPorts.
# added by Anaconda 2.3.0 installer
export PATH="~/anaconda/bin:$PATH"
And echo $PATH gives:
~/anaconda/bin:/opt/local/bin:/opt/local/sbin:/usr/local/runpkr000:~/teqc:/opt/local/bin:/opt/local/sbin:/opt/local/lib/gmt4/bin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:~/Library/TeX/texbin:/usr/texbin
I can't seem to locate where the problem is. I have been using pandas, numpy, matplotlib, scipy on my MBP for over a year and all seem to work fine (actually, the import pandas is always highlighted as red, but it works anyway). I've used Macports and Anacondas to install (as can be seen from the which -a python, it seems), and only just realised that only one of them was necessary to use. I'm a bit confused as to how to configure .profile and generally would like to tidy up this mess. My aim would be to then use conda to install another library (in this case obspy).

I followed the suggestion at the link
Where basically he has told to install anaconda using .sh variant instead of .pkg and it worked for me.

Hi instead of reinstalling everything you may add a symlink to conda (assuming everything is fine in your .profile or .bash_profile).
I did the following and worked for me:
ln -s "Applications/anaconda/bin/conda" /usr/local/bin/conda
Hope this helps
P.S. worked on OSX

Related

virtualenvwrapper.sh crashes shell

I am following the install instructions for virtualenvwrapper, described here.
I have used pip install virtualenvwrapper and it installed at the path /home/.pyenv/shims/.
But when I run the command
source /home/.pyenv/shims/virtualenvwrapper.sh the whole Konsole shuts down.
I had previously put the command in the .bashrc file and almost broke Linux because the Konsole would crash immediately after opening.
I'm using Linux OpenSuse and Python version 3.6.0.
Any ideas what could be causing the crash?
I found a solution.
source ~/.pyenv/versions/VERSION/bin/virtualenvwrapper.sh works every time.
You can't use the shims directory for some reason. Maybe since virtualenvwrapper was likely installed into the pyenv version directory. If you use the shims directory, that link could break when switching versions with pyenv. It's better to access it directly.
I'm seeing the same thing on MacOS (10.12.6).
For me the .zshrc entry which closes/ends the terminal window is:
source $HOME/.pyenv/shims/virtualenvwrapper.sh
I also would like to know why this is occurring, and how to fix it.
I have come across this problem several times now on different machines and while I don't fully understand why it happens, I have found a solution to the problem.
The problem seems to be due to mismatches in the python version being used and the pip version used to install virtualenvwrapper. I had been using the system install of python (2.7) but the pip version was for python 3.5.
To fix this, use the suggestion in this answer as follows:
python -m pip install virtualenvwrapper
Then you can source /path/to/virtualenvwrapper.sh and everything should work fine.
Sean Combs' answer works for me, too. But I didn't want to hard code a specific python version, so I use grep to build the path to virtualenvwrapper.sh dynamically.
export VIRTUALENVWRAPPER_PYTHON=$HOME/.pyenv/shims/python
source $HOME/.pyenv/versions/$($VIRTUALENVWRAPPER_PYTHON -V 2>&1 | grep -Po '(?<=Python )(.+)')/bin/virtualenvwrapper.sh
To add to Sean's answer since I don't have enough reputation to add a comment, adding
export PYENV_VERSION="$(pyenv version-name)"
source ~/.pyenv/versions/$PYENV_VERSION/bin/virtualenvwrapper.sh
to your .bashrc (or .zshrc in my case) allows you to point to the correct virtualenvwrapper.sh even if you change python versions without hardcoding or grep
I had this problem on Mac and I found that zsh crashes
with line
source ~/.pyenv/versions/$PYENV_VERSION/bin/virtualenvwrapper.sh
if you not specified VIRTUALENVWRAPPER_PYTHON variable
So this's my .zshrc (or .bashrc) config for pyenv and virtualenvwrapper on fresh user
command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"
eval "$(pyenv init -)"
export PYENV_VERSION="$(pyenv version-name)"
VIRTUALENVWRAPPER_PYTHON="$HOME/.pyenv/shims/python"
export WORKON_HOME=$HOME/.virtualenvs
export PROJECT_HOME=$HOME/Devel
source ~/.pyenv/versions/$PYENV_VERSION/bin/virtualenvwrapper.sh
# Tell pyenv-virtualenvwrapper to use pyenv when creating new Python environments
export PYENV_VIRTUALENVWRAPPER_PREFER_PYVENV="true"
# Set the pyenv shims to initialize
if command -v pyenv 1>/dev/null 2>&1; then
eval "$(pyenv init -)"
fi
I had a same problem, and I solved it by installing virtualenvwrapper with builtin python(e.g. /usr/bin/python3), not a pyenv python runtime, though the builtin one is not used in actual workspaces.
In your ~/.bashrc or ~/.zshrc, putting:
export PYENV_VERSION="$(cat $HOME/.pyenv/version)"
source "$HOME/.pyenv/versions/$PYENV_VERSION/bin/virtualenvwrapper.sh"
works for me.

Make python3 as my default python on Mac

What I'm trying to do here is to make python3 as my default python. Except the python 2.7 which automatically installed on mac, I installed python3 with homebrew. This is the website that I'm following. http://docs.python-guide.org/en/latest/starting/install3/osx/#install3-osx
I guess I followed every instruction well, got xcode freshly installed, Command line tools, and homebrew. But here's my little confusion occurs.
The script will explain what changes it will make and prompt you before the installation begins. Once you’ve installed Homebrew, insert the Homebrew directory at the top of your PATH environment variable. You can do this by adding the following line at the bottom of your ~/.profile file
export PATH=/usr/local/bin:/usr/local/sbin:$PATH
I was really confused what this was, but I concluded that I should just add this following line at the bottom of ~/.profile file. So I opened the ~/.profile file by open .profile in the terminal, and added following line at the bottom. And now it looks like this.
export PATH=/usr/local/bin:/usr/local/sbin:$PATH
# Setting PATH for Python 3.6
# The original version is saved in .profile.pysave
export PATH=/usr/local/bin:/usr/local/sbin:$PATH
And then I did brew install python, and was hoping to see python3 when I do python --version.
But it just shows me python 2.7.10. I want my default python to be python3 not 2.7
And I found a little clue from the website.
Do I have a Python 3 installed?
$ python --version
Python 3.6.4
If you still see 2.7 ensure in PATH /usr/local/bin/ takes pecedence over /usr/bin/
Maybe it has to do something with PATH? Could someone explain in simple English what PATH exactly is and how I could make my default python to be python3 when I run python --version in the terminal?
Probably the safest and easy way is to use brew and then just modify your PATH:
First update brew:
brew update
Next install python:
brew install python
That will install and symlink python3 to python, for more details do:
brew info python
Look for the Caveats:
==> Caveats
Python has been installed as
/usr/local/bin/python3
Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to
`python3`, `python3-config`, `pip3` etc., respectively, have been installed into
/usr/local/opt/python/libexec/bin
Then add to your path /usr/local/opt/python/libexec/bin:
export PATH=/usr/local/opt/python/libexec/bin:$PATH
The order of the PATH is important, by putting first the /usr/local/opt/python/libexec/bin will help to give preference to the brew install (python3) than the one is in your system located in /usr/bin/python
Before we make the changes, the default version of python in my system was python 2.7.17.
python --version
Python 2.7.17
To make python3 as default python by replacing python2 in Ubuntu.
Open Terminal
cd
nano ~/.bashrc
alias python=python3 (Add this line on top of .bashrc file)
Press ctr+o (To save the file)
Press Enter
Press ctr+x (To exit the file)
source ~/.bashrc OR . ~/.bashrc (To refresh the bashrc file)
python --version
Python 3.7.5
Changing the default python version system wide can break some applications that depend on python2. The alternative solution would be to create an alias.
If you are using zsh (the default on Mac OS) run the following from terminal:
echo 'alias python="python3"' >> ~/.zshrc
echo 'alias pip="pip3"' >> ~/.zshrc
According to this S.O. post, changing the default Python interpreter could possibly break some applications that depend on Python 2.
The post also refers to using aliasing as a solution, and this link might also be a good reference on how to do that.
Personally, I just type "Python3" before I run scripts or go into a shell environment instead of "python".

Homebrew not linking python correctly?

I installed both python 2.7.13 and python 3.6.2 with homebrew and updated my ~/.bash_profile as such:
# Homebrew
export PATH=/usr/local/bin:$PATH
Python3 was linked fine. However, "which python" would still give me
/usr/bin/python
while "which python2" produces
/usr/local/bin/python2
It looks like homebrew installed python 2 as "python2" and never linked "python" to the new installation. This is causing me a lot of trouble down the road when installing virtualenvwrapper etc.
By the way, I also did
brew link python.
Anybody know why this is and how to fix it?
Much appreciated!!
They change that behavior here
Today I’d like to announce Homebrew 1.3.0. The most significant change
since 1.2.0 is that brew install python no longer installs a python
binary without manual PATH additions and instead installs a python2
binary. This avoids overriding the system python binary by default
when installing Python as a dependency. It also paves the way to
eventually have python be Python 3.x.
You will have to symlink python to the version of python installed by homebrew that you want.
You can do:
$ln -s /usr/local/bin/python2 /usr/local/bin/python
To symlink python to the homebrew Python2.x installation or do:
$ln -s /usr/local/bin/python3 /usr/local/bin/python
to link it to the Python 3.x hombrew installation.
gsi-frank's solution solves the problem quite well but after using his solution, you might encounter problems with your pip3. Your pip3 might be linked to the old instance and therefore unusable for your new python instance.
Type which pip3 to see where your pip3's path.
If your path is linked to your new instance, then ignore the rest of this answer.
Type echo $PATH to see your current path. If it contains your old python instance's path then you will need to remove it from your .bash_profile
To solve this: check your .bash_profile and see if there is a path to your old python instance.
If the old path is in there, you can delete it.
I had this problem and here's a link to the question if needed:
How to change pip3 path after installing python with homebrew?
To find your .bash_profile:
Go to your Finder
Right click and click Go to a folder... and type ~
Press CMD + shift + . to see hidden files
Right click your .bash_profile and open in a text editor

Pip not installing Python modules to proper directory

So I downloaded a module, but when I tried to use it in a program, Python threw the error:
"ImportError: No module named markovify"
When I go to try to change my .bash_profile, it shows this:
"# Setting PATH for Python 3.5
The orginal version is saved in .bash_profile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/3.5/bin:${PATH}"
export PATH"
I've been using 2.7.10 all this time, and Terminal defaults to it. (When I type in Python, that's the version it says I'm using)
I'm trying to get pip to install modules for python 2.7.10 to a different folder.
What's weird is this: I seem to have installed pyparsing with pip and it seems to work. I tried installing markovify and it throws this error message.
What am I missing?
When I go to try to change my .bash_profile, it prints this
That suggests you're using some tool to change your profile. Did you also use that tool to install markovify? You need to be clear about your environment when you have environment questions! :-)
If you installed markovify from the command line, I'd suggest opening a new terminal and running these commands, just to make sure you're working from where you think you are:
$ python --version
Python 2.7.10
$ command -v python
/usr/bin/python
The most likely problem, it seems to me, is that you got a bit tangled up and wound up doing something other than what you intended. From a fresh start, provided you're starting with the environment you want, pip should, you know, Just Work.
I'm trying to get pip to install modules for python 2.7.10 to a different folder.
That's possible to do, but are you sure that's what you want? Usually if you're using the Python interpreter you intend to, and haven't putzed with PYTHON_PATH & friends, when you run pip, it will install to its default location, which sure enough is where Python will look for it when you say to import it.
As an experiment, you might check if markovify was somehow installed for Python 3.5. Try
$ /Library/Frameworks/Python.framework/Versions/3.5/bin/python -c 'import markovify'
(You might also want to check that the Python interpreter is in fact in that folder and has that name.)
When you're working on more than one Python version, you should work on Virtual Environments:
Virtual Env on Hitchhiker's Guide

Trouble Installing Python with Framework-style Build (OS X)

In attempting to get started learning and developing python, I've tried to follow the Python Guide to installing python on OS X, but haven't found it particularly "noob friendly." I have a new MacBook (Mtn. Lion - OS X 10.8.3) wich comes with Python 2.7.2 built in. But the guide advises installing a "framework-style build" via homebrew. So:
I installed homebrew via ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
Then it tells you to add homebrew to the top of your PATH by adding it to your ~/.bashrc file. ls -a showed that I did not have a ~/.bashrc file in my home directory. After searching Stack Overflow on how to do that, I ran nano ~/.bashrc, and inserted the line export PATH=/usr/local/bin:$PATH to the file and saved the file.
I then ran brew install python --framework and the install completed.
Then, the guide says to "add the new Python scripts directory to your PATH" so, I'm assuming that means I need to add the line it provides to my ~/.bashrc file also. So, I added export PATH=/usr/local/share/python:$PATH to my ~/.bashrc file above my previous entry.
Finally, this is where I run into trouble, it says to easy_install pip. However, when I do that I get an error 13.
So, here are the things I need some help with.
Was I correct in my assumptions about how to add homebrew and python scripts to my PATH?
Did I do something wrong or do I just need to use sudo to install pip? (I'm really sorry if the answer is already on this page but even those answers don't make total sense to me and I want to be careful and not screw something up)
After installing the framework-style build of python (which I believe was the current 2.7.3), how come running python in my terminal still shows v2.7.2?
Thanks! I appreciate any help.
I've tried to follow the Python Guide to installing python on OS X,
but haven't found it particularly "noob friendly.
Yes, I think it is misleading/outdated.
Then it tells you to add homebrew to the top of your PATH by adding it
to your ~/.bashrc file. ls -a showed that I did not have a ~/.bashrc
file in my home directory. After searching Stack Overflow on how to do
that, I ran nano ~/.bashrc, and inserted the line export
PATH=/usr/local/bin:$PATH to the file and saved the file.
On the Mac, just use ~/.profile
I then ran brew install python --framework and the install completed.
I think you don't need the --framework option unless you want to replace your Mac OS default installation and need an Mac OS Framework-style directory layout. There is no need to replace it though, the homebrew installation will take precedence anyway.
Then, the guide says to "add the new Python scripts directory to your
PATH" so, I'm assuming that means I need to add the line it provides
to my ~/.bashrc file also. So, I added export
PATH=/usr/local/share/python:$PATH to my ~/.bashrc file above my
previous entry.
Again, do it in ~/.profile. And don't forget to do a
source ~/.profile
otherwise the changes will only become active in any new terminal window, not the one you are currently using.
Finally, this is where I run into trouble, it says to easy_install
pip. However, when I do that I get an error 13.
The error shows that you try to install it your Mac OS system's default Python library (rather than in /usr/local, homebrew style), which would require root privileges. Just don't.
Also, with homebrew python, pip is already installed.
Check your path:
$ which pip
/usr/local/bin/pip
$ ls -l /usr/local/bin/pip
[..] /usr/local/bin/pip -> ../Cellar/python/2.7.3/bin/pip
Added bonus: Then do
pip install virtualenv
and use that.
And to your questions:
Was I correct in my assumptions about how to add homebrew and python
scripts to my PATH?
Yes, but use .profile and do a source .profile afterwards.
Did I do something wrong or do I just need to use sudo to install pip?
(I'm really sorry if the answer is already on this page but even those
answers don't make total sense to me and I want to be careful and not
screw something up)
You don't need sudo with homebrew, and pip is installed automatically with homebrew python.
After installing the framework-style build of python (which I believe
was the current 2.7.3), how come running python in my terminal still
shows v2.7.2?
Probably PATH not correct, do echo $PATH and check that it is correct. That is unrelated to being "framework-style" or not, though.
If you installed python with homebrew, you should already have pip installed. Try running
pip --version
to see whether and where pip is installed. Hopefully it's in a /usr/local/... path where your other homebrew things live.
Also before you install too much more with homebrew be sure to run these commands:
brew update
brew doctor
Good luck!

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