Biopython Package not recognized even when installed - python

I ran pip3 install biopython and it seemed to have been installed correctly
But when I try to run it in ipython or python3 for example
I'm quite confused because if I do the same thing with numpy or sklearn it works perfectly. Any ideas?

Notice that your environment you are using to run Python (second image) is using the Anaconda Python Distribution.
When you are installing using the command in the first image you are installing in the Python3 environment but not in the Anaconda Distribution environment.
Try running the following command to install the package in Anaconda:
conda install biopython

Related

Pytorch won't install in PyCharm on MacOS

I'm new to the MacOS and I have recently downloaded PyCharm on it. I was able to successfully install some packages like numpy, matplotlib, sympy, etc. However, Pytorch won't get installed; not through PyCharm nor through the Terminal. These are the commands I tried in the Terminal (other than attempting to install them directly from PyCharm):
pip install torch
pip install torch torchvision torchaudio
I could post the error messages but some are quite lengthy :(
I'm using Python 3.9 interpreter with pip on the latest version (20.2.4) (everything else is also up to date). Running this on the new Mac Mini (running the M1 chip).
Any ideas on what I should do? Thanks!!!
Try building from the source code, run these commands
git clone https://github.com/pytorch/pytorch.git
cd pytorch
git submodule update --init --recursive
python3 setup.py build
python3 setup.py install
Are you using a venv? If so you could try checking the box "install to user's site packages directory" in the Project Interpreter settings when you add a package.

How to install cv2?

My environment:
Ubuntu 18.0.4 LTS (also tried on 19.04)
I use/need python3 (3.6.8 installed)
I need cv2, which is a model of opencv.
I tried several receipts I found on the Internet, but nothing worked.
I tried to install as pre-compiled (sudo apt-get install python-opencv) - No error, but when I try the test:
import cv2 as cv
print(cv.__version__)
I get error module not found.
The problem seems that I have installed also anaconda. The above test uses then anaconda, and cannot find the module.
Compiling from source installed for python2, but I do need python3. (The test also uses anaconda)
One of my receipts worked till the end, but with the line:
workon OpenCV-master-py3
It gaves me the error workon not found.
I tried then to install via Conda, but that wants to downgrade Conda.
Is there a way to run it without anaconda and find a replacement for
"workon OpenCV-master-py3"
For python3 you can simply do pip3 install opencv-python and it will work.
using workon
creating virtual environment
mkvirtualenv -p python3 opencv
Inside the virtual environment.
If you are only working with images
pip install opencv-python
opencv-python
If you need support for working videos
pip install opencv-contrib-python
opencv-contrib-python
If you need a non GUI opencv
pip install opencv-python-headless
opencv-python-headless
If you need to install specific version you can use == to check the available version first like
pip install opencv-python== ,then install the version you require

How to import packages into Pycharm using PIP?

I'm trying to install a package onto Pycharm using PIP. I am running Anacondas on a Pycharm IDE. I know that you use the project interpreter to install packages and I also know that the package should be located under PyPi but when I go to the project interpreter and click add package the package I'm trying to install doesn't appear under the list of available packages.
I know that you can install the package using PIP and I have PIP installed through Anaconda although I am unsure how to run a pip command through Pycharm. I've tried typing it into the cmd console and the python code and neither seems to have any effect...
The package I'm trying to install is: https://github.com/seatgeek/fuzzywuzzy.
The pip command to install it is: pip install fuzzywuzzy but I am unsure as to where I'm supposed to run that command.
I'm fairly new at Python so any help would be much appreciated!
Thank you!
I found someone else's answer that works for me:
You need to use
import pip
pip.main(['install','packagename'])
Which allows you to manually install packages through pip using Python code.
This is guide for installing the pip packages from Python Console in Pycharm IDE.
Do not forget to run Pycharm as administrator if you are using windows OS before installing the packages.
First of all import the pacakage of pip in python console.
import pip
Installation of Package.
pip.main(['install', '<package_name>'])
Examples
The below command will upgrade the version of package setuptools.
pip.main(['install','--upgrade','setuptools'])
The below command will install the scikit-learn and numpy packages.
pip.main(['install','numpy','scikit-learn'])
The below command will uninstall the scikit-learn package.
pip.main(['uninstall','scikit-learn'])
I was with the same problem, all i did was : Configure the project interpreter to the Python3 inside the venv you are using the pip install.
Remember to activate the venv.
That's it , now you can use the pip install on pycharm or on prompot.
The problem is that even with the "venv/lib/sitepackeges" in the your project's sys.path the pycharm looks only for the packages where the project interpreter is.

Pycharm/Python OpenCV and CV2 install error

I've been trying to install both OpenCV and cv2 from both Pycharm and from the terminal as suggested using:
pip install --user opencv
pip install --user cv2
but I'm getting the following error for them:
Collecting opencv
Could not find a version that satisfies the requirement opencv (from versions: )
No matching distribution found for opencv
and
Collecting cv2
Could not find a version that satisfies the requirement cv2 (from versions: )
No matching distribution found for cv2
How can I fix these and install the packages properly? I'm using python 3.4.
You are getting those errors because opencv and cv2 are not the python package names.
These are both included as part of the opencv-python package available to install from pip.
If you are using python 2 you can install with pip:
pip install opencv-python
Or use the equivilent for python 3:
pip3 install opencv-python
After running the appropriate pip command your package should be available to use from python.
This the correct command that you need to install opencv
pip install opencv-python
if you get any error when you are trying to install the "opencv-python" package in pycharm, make sure that you have added your python path to 'System Variables' section of Environment variables in Windows.
And also check whether you have configured a valid interpreter for your project
I ran into the same problem. One issue might be OpenCV is created for Python 2.7, not 3 (not all python 2.7 libraries will work in python 3 or greater). I also don't believe you can download OpenCV directly through PyCharm's package installer. I have found luck following the instructions: OpenCV Python. Specifically:
Downloading and installing OpenCV from SourceForge
Copying the cv2.pyd file from the download (opencv\build\python\2.7\x64) into Python's site-packages folder (something like: C:\Python27\Lib\site-packages)
In PyCharm, open the python Console (Tools>Python Console) and type:import cv2, and assuming no errors print cv2.__version__
Alternatively, I have had luck using this package opencv-python, which you can straightforwardly install using pip with pip install opencv-python
Good luck!
python3.6 -m pip install opencv-python
will install cv2 in python3.6 branch
On Windows:
!pip install opencv-python
Try this. I am using Jupyter notebook (OS: Ubuntu 16.04 LTS on Google Cloud Platform + on Windows). Executed following command in the Jupyter notebook to install opencv:
!pip install opencv-contrib-python #working on both Windows and Ubuntu
After successful installation you will get following message:
Successfully installed opencv-contrib-python-4.1.0.25
Now restart the kernel and try to import opencv as:
import cv2
The same command can be used to installed opencv on Windows as well.
SOLUTION 2: try following commands to install opencv:
For Ubuntu:
Run following command from terminal:
sudo apt-get install libsm6 libxrender1 libfontconfig1
Restart Jupyter notebook kernel and execute following command:
!pip install opencv-contrib-python
NOTE: You can run all the above commands from the terminal as well without using '!'.
Keep it simple and just run.
pip install opencv-python
This is the simplest way of installing opencv.
If you still face issue, create a virtual environment and try installing opencv.
I rather use Virtualenv to install such packages rather than the entire system, saves time and effort rather than building from source.
I use virtualenvwrapper
Windows user can download
pip install virtualenvwrapper-win
https://pypi.org/project/virtualenvwrapper-win/
Linux follow
pip install opencv-python
opencv-python
If processing a video is required
pip install opencv-contrib-python
opencv-contrib-python
If you do not need GUI in Opencv
pip install opencv-contrib-python-headless
opencv-contrib-python-headless
here is a tutorial that worked for me without any problem.
Copied from the site above the important part:
Download the OpenCV version corresponding to your Python installation
from here. In my case, I’ve used
opencv_python-3.1.0-cp35-cp35m-win32.whl.
Now, open a cmd window like before. You can open this directly in your
Downloads folder if you SHIFT and right click inside it. The idea is
to open a cmd window where you’ve downloaded the above [...] file. Use
the [...] command to install [...] OpenCV:
1 pip install "opencv_python-3.1.0-cp35-cp35m-win32.whl"
Additional note: don't forget to change the name of the downloaded file in the command you use.
Apparently by installing opencv, you'll have access to cv2 too.
Installing opencv is not that direct.
You need to pre-install some packages first.
I would not recommend the unofficial package opencv-python. Does not work properly in macos and ubuntu (see this post). No idea about windows.
There are many webs explaining how to install opencv and all required packages.
For example this one.
The problem of trying to install opencv several times is that you need to uninstall completely before attempting again, or you might end having many errors.
you must install opencv-python
pip/pip3 install opencv-python
if you try import opencv-python, receive error.
Fix this error, use the import cv2
How about try some different mirrors?
If you are in China, I highly recommend you try:
sudo pip install --index https://pypi.mirrors.ustc.edu.cn/simple/ opencv-contrib-python
If not, just replace the url address to some other mirrors you like!
Good luck.
this will help you
pip3 install opencv-python
this is the snippet of successful installation
First step:
pip uninstall numpy
pip uninstall opencv-python
Second step:
pip install numpy
pip install opencv-python
I had the same problem. Here are the steps for Windows 10 users.
Open CMD: win+r then type cmd. Now,
Type pip install virtualenv
Create a Virtual Environment, Type virtualenv testopencv
Get Inside testopencv, Type cd testopencv
Activate the Virtual Environment, Type .\Scripts\activate
Now Install Opencv, Type pip install opencv-contrib-python --upgrade
Let's test Opencv, Type Python then import cv2 hit enter then type print(cv2.__version__) to check if its installed
Now, open a new cmd, win + r then type cmd, repeat step 6. If it gives you an error.
Go inside the testopencv folder, inside lib. Copy everything, go to your python directory, inside lib folder paste it and skip that are already present.
Again open a new cmd, repeat Step 6.
Hope it helps.
In win, download the py based latest numpy and Opencv from Unofficial Windows Binaries for Python Extension Packages and pip install its source in cmd. Later copy site-package folder from main py lib to venv lib.
In jetso nano this work for me.
$ git clone https://github.com/JetsonHacksNano/buildOpenCV
$ cd buildOpenCV
When I was facing this issue I used to install OpenCV in pycharm installed package panel where we can find under the settings tab. Search "OpenCV-python" and install it in the installed package panel of right interpreter.
First run from cmd
pip --version
to make sure that you have the updated version installed.
Then run
pip install opencv-python
Go through with this link: https://learnopencv.com/install-opencv-4-on-raspberry-pi/
you can install OpenCV perfectly with out any error. but the problem was it will take lot of time to install.
I had used pi3 model B+ with 32GB class10 SD card for me it took more than 12 hours for complete installation.
If you still find any error to install open-cv in your mac, try this:
opencv-python==4.2.0.34
This worked for me.

how to install python3.5 completely and remove python2.7 on Mac?

I have installed python3.5 with commands:
sudo apt-get install python3.5
after
pip install matplotlib
pip install numpy
pip install scikit-learn
It works but only on python2.7.6 installed by default. When I type "python",it show me the interactive shell of python2.7.6. I can use python3.5 by type "python3",but i can't import some library i install such as numpy, scikit-learn, matplotlib but it works in 2.7.6.
How to use all my libraries i install with python3.5 instead of 2.7.6?
pip3 will ensure you're installing packages for python3 if there's confusion with a Python 2.x installed on the same machine.
I figure out the best way to deal with it i think. I download Anaconda from this link (https://www.continuum.io/downloads). Anaconda integrates many academic libraries by default so I choose to download anaconda with the Python 3 version and all libraries going with. So now I can use it in PyCharm.
So creating a new project, I just have to choose the rep of python in my anaconda folder.
Thanks guys.

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