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Python3 ModuleNotFoundError when running from command line but works if I enter the shell

I think I'm missing something obvious here. I cloned this repo, and now have this directory structure on my computer:
When I try to run python baby_cry_detection/pc_main/train_set.py, I get a ModuleNotFoundError.
Traceback (most recent call last):
File "baby_cry_detection/pc_main/train_set.py", line 10, in <module>
from baby_cry_detection.pc_methods import Reader
ModuleNotFoundError: No module named 'baby_cry_detection'
However, if I type python and enter the interactive shell and then type the command
from baby_cry_detection.pc_methods import Reader
it imports just fine with no error. I'm completely baffled. I'm using a virtualenv and both instances are using the same python installation, and I haven't changed directories at all.

I think sys.path could be the reason that the module is not found when python command is executed. Here is how we can check if that is indeed the case:
In the train_set.py file, add import sys; print(sys.path). Looking at the error, the path may contain /path/to/baby_cry_detection/baby_cry_detection/pc_main. If that is the case, then we have found the issue which is that baby_cry_detection.pc_methods will not be found in the directory that sys.path is looking into. We'll need to append the parent baby_cry_detection directory to sys.path or use relative imports. See this answer.
The reason that python prompt successfully imports the module could be because the prompt is started in the correct parent directory. Try changing the directory to baby_cry_detection/pc_main/ and try importing the module.

Dockerized Django tests only look at first $PATH location

I'm running a Django test suite in a Docker container, and some of these tests use a program I've had to apt-get install (wkhtmltopdf). Now I can see that it's been installed correctly:
$ wkhtmltopdf --version
wkhtmltopdf 0.12.5
but for some reason the Django test can't use it. The installation location is definitely on my $PATH (third to last element):
$ echo $PATH
/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
$ find / -name wkhtmltopdf
/usr/bin/wkhtmltopdf
However when I run tests I get a stack trace ending in:
OSError: No wkhtmltopdf executable found: "/usr/local/bin/wkhtmltopdf"
If this file exists please check that this process can read it. Otherwise please install wkhtmltopdf - https://github.com/JazzCore/python-pdfkit/wiki/Installing-wkhtmltopdf
Now it's absolutely correct that there is no /usr/local/bin/wkhtmltopdf, because it got installed elsewhere (/usr/bin/) but both those locations are on $PATH.
I've tried moving /usr/bin/ to the start of $PATH, but I then get the error:
Traceback (most recent call last):
File "./manage.py", line 8, in <module>
from django.core.management import execute_from_command_line
ImportError: No module named django.core.management
presumably because it's now looking in /usr/bin/ for django when it's actually in usr/local/bin/, which is no longer the first location on $PATH.
I'm not sure if the problem is a Docker one, a Django one, a testing one, or just me misunderstanding one or more things going on here.

So it turns out that the project is using pdfkit as a wrapper for wkhtmltopdf, which includes setting the wkhtmltopdf path directly:
config = pdfkit.configuration(wkhtmltopdf=settings.WKHTMLTOPDF_BIN)
which after a quick look at the Django settings file was set to:
WKHTMLTOPDF_BIN = '/usr/local/bin/wkhtmltopdf'
Mystery solved! The fix in this case was to simply set it to the actual path desired (/usr/bin/wkhtmltopdf).

how to provide 'make directory as source root' from pyCharm to terminal

I have some problems with migrating to production:
cabox#box-codeanywhere:~/workspace/PEP$ python ./dev_scrapers/jordan.py
Traceback (most recent call last):
File "./dev_scrapers/jordan.py", line 3, in <module>
from utils import create_entity, create_id, custom_opener
ImportError: No module named utils
i have used pyCharm with button 'make directory as source root'
how to execute such command in terminal?

You should add your source root directory to PYTHONPATH:
export PYTHONPATH="${PYTHONPATH}:/your/source/root"

You can set the environment variable PYTHONPATH within the terminal as suggested by the accepted answer. This has to be done every time you start a terminal. In the case you use a virtual environment, you can place the variable assignment, like export PYTHONPATH="/your/source/root", in the file venv/bin/activate. Where venv stands for the name of the virtual environment directory.

I was able to set directory as root (and fix the unresolved import issue) doing the following:
from pycharm>Settings>Project>Project Structure select your project and from the file tree, select your django project directory then click the blue folder Source button to define the directory as your source.

Bash alias not working for Python script

Trying to set a Bash alias in order to run a Python script for Pygame.
I have the android.py acript in, /usr/local/bin/pgs4a-0.9.6/andoid.py.
Bash alias: alias pyg='python /usr/local/bin/pgs4a-0.9.6/android.py'
When I run python android.py when I am in the folder in executes just fine, but when I do it from any other folder or using the alias, I get the following error.
pyg
Traceback (most recent call last):
File "/usr/local/bin/pgs4a-0.9.6/android.py", line 11, in <module>
import interface
ImportError: No module named interface
Can anybody explain to me why this is?

Try this:
alias pyg='PYTHONPATH=/usr/local/bin/pgs4a-0.9.6 python /usr/local/bin/pgs4a-0.9.6/android.py'
That is, set your $PYTHONPATH environment variable to contain the directory with the code. You may need to adjust the PYTHONPATH to some other location, depending on where your interface package actually resides.

ImportError in Scripts directory

Using windows 7 and python 2.7. I have a package named Regetron in c:\Python27\Lib\site-packages\regetron which contains __init__.py and engine.py. When I try to run this library from the command prompt by typing regetron I get the following error:
Traceback (most recent call last):
File "C:\Python27\Scripts\regetron.py", line 6, in <module>
from regetron.engine import Regetron
File "C:\Python27\Scripts\regetron.py", line 6, in <module>
from regetron.engine import Regetron
ImportError: No module named engine
I added c:\Python27\Lib\site-packages\regetron to %PYTHONPATH% and can successfully import this module from other scripts located in other folders as well as the interactive prompt, but for some reason it refuses to run from the command prompt. What is going on?

You actually have two problems here. Fixing either one of them would actually eliminate your immediate error, but you need to fix both of them.
When I try to run this library from the command prompt by typing regetron
You shouldn't have a script named regetron and also have a module or package named regetron. Fix it by renaming your script. But if you want to understand why it's causing a problem:
The current working directory is always part of sys.path. So, you're in the directory with regetron.py in, and you run it with regetron. That means that regetron.py is on the path. So when you import regetron, it finds your script, not the package. Or, when you from regetron import engine, it finds your script, and tries to import a variable/function/class/whatever named engine from it, rather than finding the package and trying to import a module underneath it.
I added c:\Python27\Lib\site-packages\regetron to %PYTHONPATH%
Never add a package's directory to sys.path.
Since site-packages is already on your sys.path, the code in regetron/engine.py is already available as regetron.engine. You don't want it to also be available as engine. This will cause all kinds of problems.
So, rename you script to something else, remove regetron from %PYTHONPATH%, and everything will be fine.
But you may want to (re-)read the section on Packages in the tutorial.