Develop Reference

How do I run this python script?

I'm new to python, and I was wondering if you could help me run a python script. I'm trying to run a script called PunchBox from Github: https://github.com/psav/punchbox. So far, I have Python 3.9.5 and Git Bash.
In the GitHub page, it says:
To install, clone the repo, cd into it and then execute the following:
virtualenv -p python2 .pb2
source .pb2/bin/activate
pip install -U pip
pip install .
What does this mean exactly? Where do I run this code?
So far, I tried downloading the zip file from GitHub, installing Python 3.5.9, using cmd, finding the directory with cd, and running that code; but got an error:
Exception: Versioning for this project requires either an sdist tarball, or access to an upstream git repository. It's also possible that there is a mismatch between the package name in setup.cfg and the argument given to pbr.version.VersionInfo. Project name punchbox was given, but was not able to be found.
error in punchbox setup command: Error parsing C:\Users\Mi\Downloads\punchbox-master\punchbox-master\setup.cfg: Exception: Versioning for this project requires either an sdist tarball, or access to an upstream git repository. It's also possible that there is a mismatch between the package name in setup.cfg and the argument given to pbr.version.VersionInfo. Project name punchbox was given, but was not able to be found.
There's also a requirements.txt that lists additional scripts needed:
pre-commit
click
mido
pbr
PyYAML
svgwrite
Do these install automatically upon running the script for the first time?
I'm a little confused why I'm getting an error. Do you know what I'm doing wrong?
Thank you so much!
Giovanni

I assume you are new to programming. You have to write these lines in a terminal.
On Windows, it is Command Prompt or PowerShell Applications (latter preferred). On macOS, it is terminal
Copy all these lines at once, and paste them to your preferred terminal. The terminal will automatically run these one after the another.
FYI: Venv is a python package to create a virtual environment. The preceding commands set up the environment. Now install the required dependencies using this command instead of the last command (pip install .)
pip install -r requirements.txt

Based on your comment, it looks like you don't have virtualenv installed in your system. You may install it using the command pip install virtualenv.
Now, as you are using a Windows machine, you may open a Command Prompt or Windows PowerShell window and navigate to the directory where your cloned project resides.
Now, execute the following commands.
virtualenv -p python2 .pb2
.pb2\Scripts\activate.bat
pip install -U pip
pip install -r requirements.txt
Once you are done working in your virtual environment (which is named .pb2), you may close it by executing deactivate command.

#Giovanni T.
See, as far as you have installed Python and also downloaded the GitHub Repository as a zip file.
pip install -r requirements.txt
Just run this command.
Please make sure that the directory is pointing to the folder where this requirements.txt file is stored.

Cannot Use Pip Within Venv

I'm aware there are many similar questions but I have been through them all to no avail.
On Ubuntu 18.04, I have Python 2 and Python 3.6. I create a venv using the command below and attempt to install a package using pip. However, it attempts to install on the global system and not in the venv.
python3 -m venv v1
When I run 'which python' it correctly picks the python within the venv. I have checked he v1/bin folder and pip is installed. The path within the pip script is correctly pointed to toward python in the venv.
I have tried reinstalling python3 and venv, destroying and recreating the virtual environment and many other things. Wondering is there some rational way to understand and solve this.

The problem in my case was that the mounted drive I was working on was not mounted as executable. So pip couldn't be executed from within the venv on the mount.
This was confirmed because I was able to get a pip install using 'python -m pip install numpy' but when importing libraries, e.g. 'import numpy', was then faced with further error of:
multiarray_umath.cpython-36m-x86_64-linux-gnu.so: failed to map segment from shared object
which led back to the permissions issue as per github issue below. Fix for that by dvdabelle in comments then fixes dependent and original issue.
https://github.com/numpy/numpy/issues/15102
In his case, he could just switch drive. I have to use this drive. So the fix was to unmount my /data disk where I was working and remount it with exec option!
sudo umount /data
sudo mount -o exec /dev/sda4 /data
'which pip' now points to the pip in the venv correctly
Note: to make it permanent add the exec switch to the line for the drive in fstab as per https://download.tuxfamily.org/linuxvillage/Informatique/Fstab/fstab.html (make exec the last parameter in the options or user will override it) E.g.
UUID=1332d6c6-da31-4b0a-ac48-a87a39af7fec /data auto rw,user,auto,exec 0 0

virtualenv command is not found in Mac OS

I installed virtualenv using the command sudo pip install virtualenv and the installation is successful. Later, when I type virtualenv, I get the error message as following, -bash: virtualenv: command not found
The virtualenv is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages. I see the similar questions in the forum with no definitive answers.
Python is in the location /usr/local/bin/python and I have version 2.7.9. I get the following using ls -l command,
Why do I see the virtualenv is not found and how to solve the issue ?
UPDATE:
I use the command
ln -s /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/virtualenv.py /usr/local/bin/virtualenv.py to put the virtualenv.py
inside the /usr/local/bin folder. Previously, I only did the same for the virtualenv file. Now, when I put the command virtualenv in the terminal, I get
-bash: /usr/local/bin/virtualenv: Permission denied.
I later use
sudo ln -s /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/virtualenv.py /usr/local/bin/virtualenv.py
and the say message keep showing. which virtualenv still returns nothing.

Pursuant to #Jason's suggestion, try making the symbolic link for virtualenv in the /bin directory like so:
ln -s /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/virtualenv /usr/local/bin/virtualenv

Why don't re-install virtualenv? Also try to use the latest version of pip (sudo pip install -U pip).

Not sure if the answer will be useful to you, as i see the question is a few month old, but maybe it will be helpful for others.
I encountered the same problem, after installing python3.5 and pyCharm on my Mac. I moved the 3.5 folder from /Library/Frameworks/Python.framework/Versions/3.5 to /System/Library/Frameworks/Python.framework/Versions/3.5, following this guide, after disabling the System Integrity Protection first with reboot into recovery mode (boot with ctrl+R), and executing csrutil disable in the terminal. After reboot it was possible to move the python3.5 folder, and then i followed the guide, and everything worked like charm. In pyCharm i could choose the version 3.5 from /System/... instead of /Library/... (however, i still left a soft link in /Library/... to the /System folder where the python3.5 now was, just in case), and after adding the path to my zsh i could execute pip3 install virtualenv. So far so good.
Next, i tried to create the environment with virtualenv -p python3 env, and here i had the same problem as you. It seemed like the path could not be added somehow. Initially i also tried to look in the /System/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/ and include it in the $PATH, then also create softlinks to virtualenv.py as you tried too, but finally found that although all the files are in the site-packages folder, the actual executable was in /System/Library/Frameworks/Python.framework/Versions/3.5/bin/virtualenv. As the path there was included in my $PATH, i have no idea why it did not execute when typing virtualenv -p python3 env, even with sudo as you tried too, but once i typed the full path /System/Library/Frameworks/Python.framework/Versions/3.5/bin/virtualenv -p python3 env, it worked like charm again.
I still have no idea why, but it worked and now i can move on :)
Hope it helps, and hope someone can explain this better than me.

You are created the symbolic link to the wrong file. As far as I know virtualenv is installed to /Library/Frameworks/Python.framework/Versions/2.7/bin/virtualenv, (you can change the numbers for your Python version) so the command for creating the symbolic link should be:
ln -s /Library/Frameworks/Python.framework/Versions/2.7/bin/virtualenv /usr/local/bin/virtualenv

Received an error message when installing Beautiful Soup4 on Mac

I am using a Mac and I get an error message on my terminal when I try to install Beautiful Soup. I have Python 3 installed already.
This is what I did after unpacking the Beautiful Soup zip file
$ cd Users/thepredestrian/Desktop/beautifulsoup4-4.4.1
$ python setup.py install
This is the error message that appears:
Checking .pth file support in /Library/Python/2.7/site-packages/
error: can't create or remove files in install directory
The following error occurred while trying to add or remove files in
the installation directory:
[Errno 13] Permission denied: '/Library/Python/2.7/site-packages/test-easy-install-966.pth'
The installation directory you specified (via --install-dir, --prefix,
or the distutils default setting) was:
/Library/Python/2.7/site-packages/
Perhaps your account does not have write access to this directory? If the
installation directory is a system-owned directory, you may need to sign in
as the administrator or "root" account. If you do not have administrative
access to this machine, you may wish to choose a different installation
directory, preferably one that is listed in your PYTHONPATH environment
variable.
For information on other options, you may wish to consult the
documentation at:
https://pythonhosted.org/setuptools/easy_install.html
Please make the appropriate changes for your system and try again
Any advice appreciated!

Try installing with sudo.
sudo python setup.py install
An alternate way is to use virtual environment. Inside a virtual environment, you can install dependencies locally rather than system wide, so you won't need access to a root account.
pip install virtualenv
virtualenv test
cd test
source bin/activate
The first line installs virtualenv. The second line creates a virtual environment. The third and fourth line activates (starts) the virtualenv. You will notice the change in prompt. Inside virtualenv, you can install dependencies (e.g BeautifulSoup), run python scripts and so on. Once you're done, you can deactivate the environment by simply typing deactivate in the shell.

install a library for python

i'm trying to install a library for python of gene ontology programming [GOGrapher]. In the page they told me this:
$ `svn co https://projects.dbbe.musc.edu/public/GOGrapher/trunk GOGrapher`
$ cd GOGrapher
$ su -
# python setup.py install
I do everything, but in the last step a get an error
error: /usr/local/lib/python2.7/dist-packages/GOGrapher-0.0.egg-info: Permission denied
What is wrong? I'm new on this, but I do what I can.

Try
sudo python setup.py install
instead. (Works for me on Mac OS 10.7.3, while the suggested su - solution doesn't).

It is not a good idea to install things as superuser in the filesystem. In Python you can always install libraries locally.
Assuming you are already in GOGrapher directory:
$ python setup.py install --home
should install the library in your home directory. Later, you have to add the library PATH to the PYTHONPATH environment variable, so Python will know where to search for it.
$ export PYTHONPATH=$HOME/lib/python
The directory might be slightly different (lib/python2.7 or even lib/python2.7/site-packages), you can check it, tough.
To make it permanent, you should add it in your .profile, .bashrc, or whatever is the shell you are using.