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PyCharm errors on valid same-directory imports

This is somethings that has been bothering me since I started using PyCharm to program in Python. I have a two .py files, in the same directory, main.py and external.py. Inside main.py, I have import external at the top. PyCharm marks this as an error, but it runs fine both in the new zsh MacOS terminal and PyCharm itself, and I can use all the things declared in external.py as expected.
I've played around with it a bit, and (to my very limited knowledge) it seems that PyCharm detects imports like Python2. Thats a guess, though, as I am unfamiliar with that version.
Why does PyCharm do this, or am I the one to blame? If it's not my fault, how can I fix it?
My file structure is as follows:
Project-|
|-external.py
|-main.py
I want to use things from external.py in main.py, and I can, but PyCharm gives it a red underline.

From given description, it correctly imported your external module.
Did you create a folder inside your project folder?
When using subfolders for your main.py/external.py files, Pycharm might not by default correctly detect your import statement.
Pycharm should give you an error message for said import statement.
Maybe the error is not connected to the import statement but to your pycharm setup e.g. correctly setting up your python interpreter.
If you provide more information regarding your folder structure or the error message, that might help.

Please try to mark directory containing your python files as Sources Root, see https://www.jetbrains.com/help/pycharm/configuring-folders-within-a-content-root.html

ModuleNotFoundError when running script from Terminal

I have the following folder structure:
app
__init__.py
utils
__init__.py
transform.py
products
__init__.py
fish.py
In fish.py I'm importing transform as following: import utils.transform.
When I'm running fish.py from Pycharm, it works perfectly fine. However when I am running fish.py from the Terminal, I am getting error ModuleNotFoundError: No module named 'utils'.
Command I use in Terminal: from app folder python products/fish.py.
I've already looked into the solutions suggested here: Importing files from different folder, adding a path to the application folder into the sys.path helps. However I am wondering if there is any other way of making it work without adding two lines of code into the fish.py. It's because I have many scripts in the /products directory, and do not want to add 2 lines of code into each of them.
I looked into some open source projects, and I saw many examples of importing modules from a parallel folder without adding anything into sys.path, e.g. here:
https://github.com/jakubroztocil/httpie/blob/master/httpie/plugins/builtin.py#L5
How to make it work for my project in the same way?

You probably want to run python -m products.fish. The difference between that and python products/fish.py is that the former is roughly equivalent to doing import products.fish in the shell (but with __name__ set to __main__), while the latter does not have awareness of its place in a package hierarchy.

This expands on #Mad Physicist's answer.
First, assuming app is itself a package (since you added __init__.py to it) and utils and products are its subpackages, you should change the import to import app.utils.transform, and run Python from the root directory (the parent of app). The rest of this answer assumes you've done this. (If it wasn't your intention making app the root package, tell me in a comment.)
The problem is that you're running app.products.fish as if it were a script, i.e. by giving the full path of the file to the python command:
python app/products/fish.py
This makes Python think this fish.py file is a standalone script that isn't part of any package. As defined in the docs (see here, under <script>), this means that Python will search for modules in the same directory as the script, i.e. app/products/:
If the script name refers directly to a Python file, the directory
containing that file is added to the start of sys.path, and the file
is executed as the __main__ module.
But of course, the app folder is not in app/products/, so it will throw an error if you try to import app or any subpackage (e.g. app.utils).
The correct way to start a script that is part of a package is to use the -m (module) switch (reference), which takes a module path as an argument and executes that module as a script (but keeping the current working directory as a module search path):
If this option is given, [...] the current directory
will be added to the start of sys.path.
So you should use the following to start your program:
python -m app.products.fish
Now when app.products.fish tries to import the app.utils.transform module, it will search for app in your current working directory (which contains the app/... tree) and succeed.
As a personal recommendation: don't put runnable scripts inside packages. Use packages only to store all the logic and functionality (functions, classes, constants, etc.) and write a separate script to run your application as you wish, putting it outside the package. This will save you from this kind of problems (including the double import trap), and has also the advantage that you can write several run configurations for the same package by just making a separate startup script for each.

Pycharm run the code adding the current working dir to PYTHONPATH

Trying to figure this out, because there is an inconsistency between when I run the code from Pycharm and from terminal.
Pycharm add automatically the current working directory; so if I add a module that is contained in my CWD, that is not in Pythonpath, it works just fine.
But when running from terminal, Python does complain, because my import statements refer to modules that are not reachable, because the CWD is not added to PYTHONPATH (I did verify this printing out the content of the variable, while running from Pycharm and from Terminal).
So at this point I am assuming that in my startup code, I need to add to Pythonpath the current directory, or this is not correct? I have no way to tell where the final user may put my code in; I just assume that the whole directory containing all my different modules, is located in a specific place.
To be more specific, this is where I am at:
my CWD when I run from Pycharm is /apps/myapp/logic/, I run the script after cd in that directory, and I call the script with ./myscript.py
The script has the #!/usr/bin/python3 line as first line, instead of running it with python3 -m myscript.py
The error I get, is when loading a module that is either in the same directory of my script (/apps/myapp/logic/) or one level above (/apps/myapp/); sadly the module load happen before my __main__ is running; so I can't add to sys.path the current directory from which the script run.
All these issues are not happening if I just run the script from Pycharm

After various trial and error, and thanks to the info that I did get from the comments; I did find 2 ways to solve the issue.
1) Create a shell script or another python script, which is adding the current directory (where all the files lives), and have no import in this file. Then the script call the script that has the main function.
2) On the top of the module, right after import sys, add the statement to add the path, in this way the current directory will be added to the PATH and it will be accessible, when the import try to access the module.
Neither look very nice, but this is all that I was able to find, to solve the issue. Pretty sure there is a more elegant way to do so

How to import python file located in same subdirectory in a pycharm project

I have an input error in pycharm when debugging and running.
My project structure is rooted properly, etc./HW3/. so that HW3 is the root directory.
I have a subfolder in HW3, util, and a file, util/util.py. I have another file in util called run_tests.py.
In run_tests.py, I have the following import structure,
from util.util import my_functions, etc.
This yields an input error, from util.util import load_dataset,proportionate_sample
ImportError: No module named 'util.util'; 'util' is not a package
However, in the exact same project, in another directory (same level as util) called data, I have a file data/data_prep.py, which also imports functions from util/util.py using a similar import statement...and it runs without any problems.
Obviously, I am doing this in the course of doing a homework, so please understand: this is ancillary to the scope of the homework.
The problem goes away when I move the file to another directory. So I guess this question is How do I import a python file located in the same directory in a pycharm project? Because pycharm raises an error if I just do import util and prompts me to use the full name from the root.

Recommended Way:
Make sure to set the working folder as Sources.
You can do it in Pycharm -> Preferences -> Project: XYZ -> Project Structure
Select your working folder and mark it as Sources. Then Pycharm recognize the working folder as a Source folder for the project and you will be able to simply add other files within that folder by using
import filename.py
or
from filename.py import mudule1
=================
Not recommended way:
In Pycharmyou can simply add . before the .py file which you are going to import it from the same folder. In your case it will be
from .util import my_functions
Resource
There is a good reference also for more information with example how to implement Package Relative Imports. I would highly recommend to check this page.
Package Relative Imports

If you don't have an __init__.py create one and add this line
from util.util import my_function
then you can easily import the module in your scripts
the __init__.py tells python that it should treat that folder as a python package, it can also be used to import/load modules too.
in most cases the __init__.py is empty.
Quoting the docs:
The __init__.py files are required to make Python treat the
directories as containing packages; this is done to prevent
directories with a common name, such as string, from unintentionally
hiding valid modules that occur later on the module search path. In
the simplest case, __init__.py can just be an empty file, but it can
also execute initialization code for the package or set the __all__
variable, described later.

Right-click on the folder which you want to be marked as the source > Mark Directory as > Source root.

In my case, it worked only when I omit the extension. Example:
import filename

Note: May be a bit unrelated.
I was facing the same issue but I was unable to import a module in the same directory (rather than subdirectory as asked by OP) when running a jupyter notebook (here the directory didn't have __init__.py). Strangely, I had setup python path and interpreter location and everything. None of the other answers helped but changing the directory in python did.
import os
os.chdir(/path/to/your/directory/)
I'm using PyCharm 2017.3 on Ubuntu 16.04

I had the same issue with pycharm, but the actual mistake was that the file I was trying to import didn't have a .py extension, even though I was able to run it as a standalone script. Look in the explorer window and make sure it has a .py extension. If not, right click on the file in the explorer window, pick refactor, and then rename it with a .py extension.

In Pycharm go to "Run - Configuration" and uncheck
'Add Content root to Pythonpath' and
'Add source roots to Pythonpath',
then use
from filename import functionname

For me the issue was, the source directory was marked correctly, but my file to import was named starting with numeric value. Resolved by renaming it.
import 01_MyModuleToImport
to
import MyModuleToImport

PyCharm error: 'No Module' when trying to import own module (python script)

I have written a module (a file my_mod.py file residing in the folder my_module).
Currently, I am working in the file cool_script.py that resides in the folder cur_proj. I have opened the folder in PyCharm using File -- open (and I assume, hence, it is a PyCharm project).
In ProjectView (CMD-7), I can see my project cur_proj (in red) and under "External Libraries" I do see my_module. In cool_script.py, I can write
from my_module import my_mod as mm
and PyCharm even makes suggestion for my_mod. So far so good.
However, when I try to run cool_script.py, PyCharm tells me
"No module named my_module"
This seems strange to me, because
A) in the terminal (OS 10.10.2), in python, I can import the module no problem -- there is a corresponding entry in the PYTHONPATH in .bashrc
B) in PyCharm -- Settings -- Project cur_proj -- Project Interpreter -- CogWheel next to python interpreter -- more -- show paths for selected interpreter icon, the paths from PYTHONPATH do appear (as I think they should)
Hence, why do I get the error when I try to run cool_script.py? -- What am I missing?
Notes:
I am not declaring a different / special python version at the top of cool_script.py
I made sure that the path to my_module is correct
I put __init__.py files (empty files) both in my_module and in cur_proj
I am not using virtualenv
Addendum 2015-Feb-25
When I go in PyCharm to Run -- Edit Configurations, for my current project, there are two options that are selected with a check mark: "Add content roots to PYTHONPATH" and "Add source roots to PYTHONPATH". When I have both unchecked, I can load my module.
So it works now -- but why?
Further questions emerged:
What are "content roots" and what are "source roots"? And why does adding something to the PYTHONPATH make it somehow break?
should I uncheck both of those options all the time (so also in the defaults, not only the project specific configurations (left panel of the Run/Debug Configurations dialog)?

If your own module is in the same path, you need mark the path as Sources Root. In the project explorer, right-click on the directory that you want import. Then select Mark Directory As and select Sources Root.

So if you go to
-> Setting -> Project:My_project -> Project Structure,
Just the directory in which the source code is available and mark it as "Sources" (You can see it on the same window). The directory with source code should turn blue. Now u can import in modules residing in same directory.

PyCharm Community/Professional 2018.2.1
I was having this problem just now and I was able to solve it in sort of a similar way that #Beatriz Fonseca and #Julie pointed out.
If you go to File -> Settings -> Project: YourProjectName -> Project Structure, you'll have a directory layout of the project you're currently working in. You'll have to go through your directories and label them as being either the Source directory for all your Source files, or as a Resource folder for files that are strictly for importing.
You'll also want to make sure that you place __init__.py files within your resource directories, or really anywhere that you want to import from, and it'll work perfectly fine.

What I tried is to source the location where my files are.
e.g. E:\git_projects\My_project\__init__.py is my location.
I went to File -> Setting -> Project:My_project -> Project Structure and added the content root to about mention place E:\git_projects\My_project
it worked for me.

Always mark as source root the directory ABOVE the import!
So if the structure is
parent_folder/src/module.py
you must put something like:
from src.module import function_inside_module
and have parent_folder marked as "source folder" in PyCharm

I was getting the error with "Add source roots to PYTHONPATH" as well. My problem was that I had two folders with the same name, like project/subproject1/thing/src and project/subproject2/thing/src and I had both of them marked as source root. When I renamed one of the "thing" folders to "thing1" (any unique name), it worked.
Maybe if PyCharm automatically adds selected source roots, it doesn't use the full path and hence mixes up folders with the same name.

my_module is a folder not a module and you can't import a folder, try moving my_mod.py to the same folder as the cool_script.py and then doimport my_mod as mm. This is because python only looks in the current directory and sys.path, and so wont find my_mod.py unless it's in the same directory
Or you can look here for an answer telling you how to import from other directories.
As to your other questions, I do not know as I do not use PyCharm.

The key confusing step that must be done is to recreate the run configuration for the source file that you're trying to execute, so that the IDE picks up the new paths.
The way that actually worked for me was to go to Run/Edit Configurations..., select the configuration for the file that you're trying to run on the left side, uncheck the "Add source roots to PYTHONPATH" box, save, and then go back and check the box and save. THEN it would work.

This can be caused when Python interpreter can't find your code. You have to mention explicitly to Python to find your code in this location.
To do so:
Go to your python console
Add sys.path.extend(['your module location']) to Python console.
In your case:
Go to your python console,
On the start, write the following code:
import sys
sys.path.extend([my module URI location])
Once you have written this statement you can run following command:
from mymodule import functions

The solution for this problem without having to Mark Directory as Source Root is to Edit Run Configurations and in Execution select the option "Redirect input from" and choose script you want to run. This works because it is then treated as if the script was run interactively in this directory. However Python will still mark the module name with an error "no module named x":
When the interpreter executes the import statement, it searches for x.py in a list of directories assembled from the following sources:
The directory from which the input script was run or the current directory if the interpreter is being run interactively
The list of directories contained in the PYTHONPATH environment variable, if it is set.
An installation-dependent list of directories configured at the time Python is installed, in my case usr/lib/python3.6 on Ubuntu.

Content roots are folders holding your project code while source roots are defined as same too. The only difference i came to understand was that the code in source roots is built before the code in the content root.
Unchecking them wouldn't affect the runtime till the point you're not making separate modules in your package which are manually connected to Django. That means if any of your files do not hold the 'from django import...' or any of the function isn't called via django, unchecking these 2 options will result in a malfunction.
Update - the problem only arises when using Virtual Environmanet, and only when controlling the project via the provided terminal. Cause the terminal still works via the default system pyhtonpath and not the virtual env. while the python django control panel works fine.

PyCharm 2021.2.4 -- March 4th, 2022
Solved it by marking the source directory as "Source". Accomplished it by
right clicking on the source directory in the Project structure on the left of the IDE. I had a code source named src/.
navigate to "Mark Directory as".
select "Source" as directory type.
In short,
src -> Mark Directory as -> Source

This can occur if you are running a python file with the same name as one of its parent directories and try to import another
e.g.
Say you have files
my_project/processing/method1/processing.py
my_project/processing/algorithms/predict.py
And in processing.py you do something like:
from my_project.processing.algorithms.predict import Predict
it will throw the error

ln -s . someProject
If you have someDirectory/someProjectDir and two files, file1.py and file2.py, and file1.py tries to import with this line
from someProjectDir import file2
It won't work, even if you have designated the someProjectDir as a source directory, and even if it shows in preferences, project, project structure menu as a content root. The only way it will work is by linking the project as show above (unix command, works in mac, not sure of use or syntax for Windows).
There seems some mechanism where Pycharm does this automatically either in checkout from version control or adding as context root, since the soft link was created by Pycharm in a dependent project. Hence, just copying the same, although the weird replication of directory is annoying and necessity is perplexing. Also in the dependency where auto created, it doesn't show as new directory under version control. Perhaps comparison of .idea files will reveal more.

try installing the missing modules using the "terminal" on pycharm
python -m pip install your-module

Pycharm 2017.1.1
Click on View->ToolBar & View->Tool Buttons
On the left pane Project would be visible, right click on it and
press Autoscroll to source
and then run your code.
This worked for me.

The answer that worked for me was indeed what OP mentions in his 2015 update: uncheck these two boxes in your Python run config:
"Add content roots to PYTHONPATH"
"Add source roots to PYTHONPATH"
I already had the run config set to use the proper venv, so PyCharm doing additional work to add things to the path was not necessary. Instead it was causing errors.