I'm following the directions from the Biopython website (http://biopython.org/wiki/Download) but I keep getting an error during installation. I have python 2.7 installed on my laptop.
python2.7 -m pip install biopython
I just get the error:
No module named pip
I looked up this error and tried something stack overflow suggested:
sudo apt-get install python-pip
But I just got another error:
sudo: apt-get: command not found
As long as you have Python 2.7.9 onwards this should automatically install pip for you:
python -m ensurepip
It would be useful to know what Operating System you have to help improve the instructions here.
Many dependency issues are solved here at Annaconda where you fetch python, lots of nice libs, etc.. Install it accordingly to your platform.. windows, Linux or Mac OS.
Biopython is installed by Annaconda by default (including matplotlib and other dependencies)... if I recall correctly. Otherwise its from commandline conda search biopython and or conda install pip. And then commandline pip install biopython.
Related
I'm working on a Pyramid project that has to be deployed in a Debian 7 server.
The Debian 7 server has the python version 2.7.3 as from the archives repositories.
After creating a virtual environment with virtualenv command the pip version installed in this virtualenv is 1.1.
First thing noted: I can't upgrade pip with pip install --upgrade pip. The version is not updated and remains in 1.1 version.
After installing the OS packages needed to install the project I ran python setup.py install but I get the error:
Searching for zipp==0.5
Reading http://pypi.python.org/simple/zipp/
Couldn't find index page for 'zipp' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading http://pypi.python.org/simple/
No local packages or download links found for zipp==0.5
error: Could not find suitable distribution for Requirement.parse('zipp==0.5')
So, the python setup.py install command could not recognize the zipp package.
I thought that this was related to the older version of pip (1.1). So I could update pip version successfully using the index-url option:
$ pip install --index-url https://pypi.python.org/simple --upgrade pip
That updated pip version from 1.1 to 20.3b1. Then I tried python setup.py install again, but the same error occurred.
What I could see is that, after updating pip version, the zipp==0.5.0 package is installed if I ran pip install zipp==0.5.
I'm new to Pyramid and the package installing using the setup.py module. I'm not understanding why I can install the zipp package with pip and can't with python setup.py install.
I'm not putting the content of setup.py here because I think it's not a problem of the setup.py script. With more recent versions of python and pip in an Ubuntu 18.04 machine the setup.py works like a charm.
Someone could explain how to solve this issue?
When you run python setup.py install directly, you are not using pip, so the version of pip you have installed is irrelevant. This command is antiquated, should not be used, etc, etc. The right answer is to use pip install . as a replacement for python setup.py install and to use pip install -e . as a replacement for python setup.py develop.
With respect to what you're seeing, when you run python setup.py install this using the version of easy_install bundled with setuptools to talk to PyPI and install dependencies. This should be avoided for a lot of reasons but just know that to override urls it uses they go in ~/.pydistutils.cfg and have nothing to do with pip. HTTPS is one problem that you looked at, another is that old versions of Python do not have the right CA trust store, nor support the minimum required TLS 1.2 to handshake with PyPI. So expect lots of problems using old tools - at the very least try to use pip instead of easy_install.
So I tried to install pip using the get-pip.py file, and when I ran the file, terminal told me I already had pip installed on 2.7. However, when I try to find the version of my pip, terminal tells me pip doesn't exist and points to a version of 3.5 I have installed. Clearly my issue is that I have pip installed on v2.7 but the pip command is linked to v3.5. Any clues on how to fix?
Here's a picture of my terminal output:
To install a package in a particular version of python, use the following commands always:
For python 2.x:
sudo python -m pip install [package]
For python 3.x:
sudo python3 -m pip install [package]
This should resolve the doubt of which python version is the given package getting installed for.
Note: This is assuming you have not created aliases for the python command
I am working on small python scripts. Basically i am not a python programmer and very new to it. Recently i have been working on IOT protocol MQTT. I have installed a open source MQTT clinet based on python3 in my raspberypi board. And now i am facing a problem. I have python 2.7 and 3.2 installed.
My MQTT client work with Python3.x and i want to use pyserial library also which i am not able to , i am getting a error
Serial module not found
I goggled a bit and end up here.. Now it say that you need to install pip3 in order to install pyserial for python3.x.
I tried to install pip3 using this link , but end up installing pip2 using
pip install -U pip
I feel totally being messed up now. I just want to use pyserial while working with python3.x version.Can any one suggest me how?
Edit 1:
On Linux, Mac OS X and other POSIX systems, use the versioned Python commands in combination with the -m switch to run the appropriate copy of pip:
python2 -m pip install SomePackage # default Python 2
python2.7 -m pip install SomePackage # specifically Python 2.7
python3 -m pip install SomePackage # default Python 3
python3.4 -m pip install SomePackage # specifically Python 3.4
I recently came through this documentation given here . But it even give a error to me /usr/bin/python3 : NO module named pip. main : 'pip' is a package and cannot be installed directly.
Assuming you're using raspbian on your pi, you could install pip3 from the normal repositories:
apt-get install python3-pip
You can get the serial module the same way:
apt-get install python3-serial
I succeeded installing pyserial2.7 on a Mac running Yosemite and Python3.4
I entered the pyserial-x.y directory and run:
python3 setup.py install
I got lot of errors that I corrected one by one by editing the files containing the syntax errors. Only 2 types of errors are encountered:
- print needs ()
- except needs as instead of ,
So by correcting the dozen of errors with some patience, installation finish correctly.
I wonder why a syntactically correct version for Python3 is not ready!
I've just learned how to use virtualenv and I installed Django 1.4.5. I'm assuming that the virtualenv created a clean slate for me to work on so with the Django 1.4.5 installed, I copied all my previous files into the virtualenv environment.
I tried to run the server but I get an error saying "no module named MySQLdb". I think this means that I forgot to install MySQL-python. I tried to install it via
pip install MySQL-python
But I get this error
Downloading/unpacking MySQL-python
Running setup.py egg_info for package MySQL-python
The required version of distribute (>=0.6.28) is not available,
and can't be installed while this script is running. Please
install a more recent version first, using
'easy_install -U distribute'.
(Currently using distribute 0.6.24 (/home/bradford/Development/Django/django_1.4.5/lib/python2.7/site-packages/distribute-0.6.24-py2.7.egg))
Complete output from command python setup.py egg_info:
The required version of distribute (>=0.6.28) is not available,
and can't be installed while this script is running. Please
install a more recent version first, using
'easy_install -U distribute'.
(Currently using distribute 0.6.24 (/home/bradford/Development/Django/django_1.4.5/lib/python2.7/site-packages/distribute-0.6.24-py2.7.egg))
----------------------------------------
Command python setup.py egg_info failed with error code 2 in /home/bradford/Development/Django/django_1.4.5/build/MySQL-python
Not quite sure how to go about fixing this problem =/ any help much appreciated!
I recently had exactly this issue (just not in relation to Django). In my case I am developing on Ubuntu 12.04 using the default pip and distribute versions, which are basically a little out of date for MySQL-python.
Because you are working in an isolated virtualenv, you can safely follow the suggested instruction without affecting your Python installation.
So you can...
workon your_virtualenv #activate your virtualenv, you do use virtualenvwrapper, right?
easy_install -U distribute #update distribute on your virtualenv
pip install MySQL-python #install your package
If for some reason upgrading distribute is not an option, you could try installing an older version of MySQL-python as follows (you'd have to check this version is compatible with your version of Django):
pip install MySQL-python==x.y.z #where x.y.z is the version you want
Spent an hour looking through stackoverflow. Evntually found answer in the other question. This is what saved me:
sudo apt-get install libmysqlclient-dev
mysql_config goes with the package.
When doing in a virtualenv :
pip install MySQL-python
I got
EnvironmentError: mysql_config not found
To install mysql_config, as Artem Fedosov said, first install
sudo apt-get install libmysqlclient-dev
then everything works fine in virtualenv
MySQL driver for Python (mysql-python) needs libmysqlclient-dev. You can get it with:
sudo apt-get update
sudo apt-get install libmysqlclient-dev
If python-dev is not installed, you may have to install it too:
sudo apt-get install python-dev
Now you can install MySQL driver:
pip install mysql-python
Here is a more detailed documentation for MySQL in Django:
http://codex.themedelta.com/how-to-install-django-with-mysql-in-a-virtualenv-on-linux/
I had to do this:
pip install mysql-python
inside the virtualenv
The commands are always run in ubuntu:
easy_install -U distribute
later
sudo apt-get install libmysqlclient-dev
and finally
pip install MySQL-python
The suggested solutions didn't work out for me, because I still got compilation errors after running
`$ sudo apt-get install libmysqlclient-dev`
so I had to run
apt-get install python-dev
Then everything worked fine for me with
apt-get install python-dev
Try this:
Version Python 2.7
MySQL-python package, you should use either MySQL_python‑1.2.5‑cp27‑none‑win32.whl or
MySQL_python‑1.2.5‑cp27‑none‑win_amd64.whl depending on whether you have installed 32-bit or 64-bit Python.
pip install MySQL_python‑1.2.5‑cp27‑none‑win32.whl
if you are using mysqlclient package, then use
mysqlclient‑1.4.6‑cp27‑cp27m‑win32.whl or
mysqlclient‑1.4.6‑cp27‑cp27m‑win_amd64.whl
pip install mysqlclient‑1.4.6‑cp27‑cp27m‑win32.whl
https://www.lfd.uci.edu/~gohlke/pythonlibs/#mysqlclient
sudo apt-get install python-Orange
or
sudo apt-get install python-orange
doesn't work
sudo python setup.py install
sudo python setup.py build
is not working as well.
Can anyone help??
Python has two tools for easy installation of all programs that are listed on the Python Package Index, also known as PyPi: These are easy_install and pip. Both retrieve very recent versions of Orange (and of any other package that is updating its PyPi entry regularly).
I installed Orange on Ubuntu 12.04 (LTS) with
pip install orange.
You will see lots of log lines indicating that Pip is downloading and compiling Orange for you. Simply wait. When pip is ready, fire up python and try to import orange. If that works, quit python and try the GUI with python /usr/local/lib/python2.7/dist-packages/Orange/OrangeCanvas/orngCanvas.pyw (you probably want to create a shell alias or bash script for that one :-)
NOTE: on 12.04 I needed to first upgrade 'distribute' itself with sudo easy_install -U distribute but this was clearly indicated by pip.
https://pypi.python.org/pypi/Orange/2.6/
You need to extract the dowloaded tarball on that page to a folder and then change directory to that folder. Then the sudo python setup.py... instructions will work (but you should 'build' the application before you 'install' it).
go to the given link "https://pypi.python.org/pypi/Orange/2.6/"
download the package and extract the file
install with given command
python setup.py build
python setup.py install
note:- during installation make sure that your net is working because it downloads required packages. Also it may ask for C++ or gcc compilers while installing and could be terminate just read the errors care fully and install requires packages from the synaptic package manage in ubuntu.