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Importing module from a directory above current working directory

First of all, there are a bunch of solutions on stackoverflow regarding this but from the ones I tried none of them is working. I am working on a remote machine (linux). I am prototyping within the dir-2/module_2.py file using an ipython interpreter. Also I am trying to avoid using absolute paths as the absolute path in this remote machine is long and ugly, and I want my code to run on other machines upon download.
My directory structure is as follows:
/project-dir/
-/dir-1/
-/__ init__.py
-/module_1.py
-/dir-2/
-/__ init__.py
-/module_2.py
-/module_3.py
Now I want to import module_1 from module_2. However the solution mentioned in this stackoverflow post: link of using
sys.path.append('../..')
import module_2
Does not work. I get the error: ModuleNotFoundError: No module named 'module_1'
Moreover, within the ipython interpreter things like import .module_3 within module_2 throws error:
import .module_3
^ SyntaxError: invalid syntax
Isn't the dot operator supposed to work within the same directory as well. Overall I am quite confused by the importing mechanism. Any help with the initial problem is greatly appreciated! Thanks a lot!

Why it didn't work?
If you run the module1.py file and you want to import module2 then you need something like
sys.path.append("../dir-2")
If you use sys.path.append("../..") then the folder you added to the path is the folder containing project-dirand there is notmodule2.py` file inside it.
The syntax import .module_3 is for relative imports. if you tried to execute module2.py and it contains import .module_3 it does not work because you are using module2.py as a script. To use relative imports you need to treat both module2.py and module_3.py as modules. That is, some other file imports module2 and module2 import something from module3 using this syntax.
Suggestion on how you can proceed
One possible solution that solves both problems is property organizing the project and (optionally, ut a good idea) packaging your library (that is, make your code "installable"). Then, once your library is installed (in the virtual environment you are working) you don't need hacky sys.path solutions. You will be able to import your library from any folder.
Furthermore, don't treat your modules as scripts (don't run your modules). Use a separate python file as your "executable" (or entry point) and import everything you need from there. With this, relative imports in your module*.py files will work correctly and you don't get confused.
A possible directory structure could be
/project-dir/
- apps/
- main.py
- yourlib/
-/__ init__.py
-/dir-1/
-/__ init__.py
-/module_1.py
-/dir-2/
-/__ init__.py
-/module_2.py
-/module_3.py
Notice that the the yourlib folder as well as subfolders contain an __init__.py file. With this structure, you only run main.py (the name does not need to be main.py).
Case 1: You don't want to package your library
If you don't want to package your library, then you can add sys.path.append("../") in main.py to add "the project-dir/ folder to the path. With that your yourlib library will be "importable" in main.py. You can do something like from yourlib import module_2 and it will work correctly (and module_2 can use relative imports). Alternatively, you can also directly put main.py in the project-dir/ folder and you don't need to change sys.path at all, since project-dir/ will be the "working directory" in that case.
Note that you can also have a tests folder inside project-dir and to run a test file you can do the same as you did to run main.py.
Case 2: You want to package your library
The previous solution already solves your problems, but going the extra mile adds some benefits, such as dependency management and no need to change sys.path no matter where you are. There are several options to package your library and I will show one option using poetry due to its simplicity.
After installing poetry, you can run the command below in a terminal to create a new project
poetry new mylib
This creates the following folder structure
mylib/
- README.rst
- mylib/
- __init__.py
- pyproject.toml
- tests
You can then add the apps folder if you want, as well as subfolders inside mylib/ (each with a __init__.py file).
The pyproject.toml file specifies the dependencies and project metadata. You can edit it by hand and/or use poetry to add new dependencies, such as
poetry add pandas
poetry add --dev mypy
to add pandas as a dependency and mypy as a development dependency, for instance. After that, you can run
poetry build
to create a virtual environment and install your library in it. You can activate the virtual environment with poetry shell and you will be able to import your library from anywhere. Note that you can change your library files without the need to run poetry build again.
At last, if you want to publish your library in PyPi for everyone to see you can use
poetry publish --username your_pypi_username --password _passowrd_
TL; DR
Use an organized project structure with a clear place for the scripts you execute. Particularly, it is better if the script you execute is outside the folder with your modules. Also, don't run a module as a script (otherwise you can't use relative imports).

Importing from sibling directories (python 3)

I can't figure out how to import modules from sibling directories in Python 3 using absolute imports.
modify the sys.path.
turn the directory into a pip installable package via __init__.py and setup.py.
For option 1. I figured out how to import modules from sibling directories by modifying the sys.path, but this method seems a little hackey to me. Also, I've read that it is not preferred. Why? Is there something inherently wrong or dangerous about modifying the sys.path?
For option 2. What exactly do I need to do make my package pip installable? I've alreay created my __init__.py file, but it seems that I need to create and configure a setup.py script to prepare my package for distribution? I'm still in the development mode, so is this really the best/pythonic method? If it is, then do I just type python setup.py install into my terminal after creating the setup.py?
Edit: I'm now trying to figure this out using absolute imports as python 3 does support relative imports.

From what I've read, Python 3 does not support relative imports
It does.
To import myproject/foo/__init__.py from myproject/bar/baz.py, you can use this:
from .. import foo
Or if you want to import an object/module in foo:
from ..foo import object
This requires myproject to be a package, so myproject/__init__.py has to exist.

python path during development of a package

Let's say my project structure looks like this:
app/
main.py
modules/
__init__.py
validation.py
configuration.py
modules package contains reusable code.
main.py executes main application logic.
When I try this in main.py
from modules import validation
I get an error which says that import inside of the validation failed. Validation tries to import configuration and I get 'no module named configuration'
I am using Anaconda distribution on windows.
What is the best way of handling PYTHONPATH during development of the package ?
Is there a way to utilize virtualenv (or conda env) in order to get package, that is in development,on the PYTHONPATH without changing sys.path from the code ?
What is the preferred practice when developing a package ?
I've also tried adding modules (folder) package to the lib/site-packages but it still didn't work.

Change your import in validation.py to:
from . import configuration
This is needed for Python 3 but also works with Python 2.

Change cwd before running tests

I have a bunch of unittest test cases in separate directories. There is also a directory which just contains helper scripts for the tests. So my file tree looks like this
test_dir1
test_dir2
test_dir3
helper_scripts
Each python file in test_dir* will have these lines:
import sys
sys.path.append('../helper_scripts')
import helper_script
This all works fine, as long as I run the tests from within their directory. However, I would like to be at the project root and just run:
py.test
and have it traverse all the directories and run each test it finds. The problem is that the tests are being run from the wrong directory, so the sys.path.append doesn't append the helper_scripts directory, it appends the parent of the project root. This makes all the imports fail with an Import Error.
Is there a way to tell py.test to run the test scripts from their directory? ie. change the cwd before executing them? If not, is there another test runner I can use that will?

What I usually do is structure my project like this:
myproject/
setup.py
myproject/
__init__.py
mymodule.py
tests/
__init__.py
test_dir1/
test_mymodule.py
helper_scripts/
__init__.py
helper_script.py
For running tests, I use a virtualenv with myproject installed in development mode using one of the following commands in the myproject root directory:
pip install -e .
python setup.py develop
Now in test_mymodule.py I can just say
from myproject.tests.helper_scripts import helper_script
I can then just run pytest and there's no need to change the working directory in tests at all.
See Pytest's Good Integration Practices for a great summary of pros and cons for different project directory structures.

os.chdir("newdir")
will change your current working directory

I would suggest that you instead configure your environment so that import helper_scripts will work regardless of the current directory. This is the recommended approach.
If you absolutely must though, you can use relative imports instead:
from .. import helper_script

Importing correctly with pytest

I just got set up to use pytest with Python 2.6. It has worked well so far with the exception of handling "import" statements: I can't seem to get pytest to respond to imports in the same way that my program does.
My directory structure is as follows:
src/
main.py
util.py
test/
test_util.py
geom/
vector.py
region.py
test/
test_vector.py
test_region.py
To run, I call python main.py from src/.
In main.py, I import both vector and region with
from geom.region import Region
from geom.vector import Vector
In vector.py, I import region with
from geom.region import Region
These all work fine when I run the code in a standard run. However, when I call "py.test" from src/, it consistently exits with import errors.
Some Problems and My Solution Attempts
My first problem was that, when running "test/test_foo.py", py.test could not "import foo.py" directly. I solved this by using the "imp" tool. In "test_util.py":
import imp
util = imp.load_source("util", "util.py")
This works great for many files. It also seems to imply that when pytest is running "path/test/test_foo.py" to test "path/foo.py", it is based in the directory "path".
However, this fails for "test_vector.py". Pytest can find and import the vector module, but it cannot locate any of vector's imports. The following imports (from "vector.py") both fail when using pytest:
from geom.region import *
from region import *
These both give errors of the form
ImportError: No module named [geom.region / region]
I don't know what to do next to solve this problem; my understanding of imports in Python is limited.
What is the proper way to handle imports when using pytest?
Edit: Extremely Hacky Solution
In vector.py, I changed the import statement from
from geom.region import Region
to simply
from region import Region
This makes the import relative to the directory of "vector.py".
Next, in "test/test_vector.py", I add the directory of "vector.py" to the path as follows:
import sys, os
sys.path.append(os.path.realpath(os.path.dirname(__file__)+"/.."))
This enables Python to find "../region.py" from "geom/test/test_vector.py".
This works, but it seems extremely problematic because I am adding a ton of new directories to the path. What I'm looking for is either
1) An import strategy that is compatible with pytest, or
2) An option in pytest that makes it compatible with my import strategy
So I am leaving this question open for answers of these kinds.

The issue here is that Pytest walks the filesystem to discover files that contain tests, but then needs to generate a module name that will cause import to load that file. (Remember, files are not modules.)
Pytest comes up with this test package name by finding the first directory at or above the level of the file that does not include an __init__.py file and declaring that the "basedir" for the module tree containing a module generated from this file. It then adds the basedir to sys.path and imports using the module name that will find that file relative to the basedir.
There are some implications of this of which you should beware:
The basepath may not match your intended basepath in which case the module will have a name that doesn't match what you would normally use. E.g., what you think of as geom.test.test_vector will actually be named just test_vector during the Pytest run because it found no __init__.py in src/geom/test/ and so added that directory to sys.path.
You may run into module naming collisions if two files in different directories have the same name. For example, lacking __init__.py files anywhere, adding geom/test/test_util.py will conflict with test/test_util.py because both are loaded as import test_util.py, with both test/ and geom/test/ in the path.
The system you're using here, without explicit __init__.py modules, is having Python create implicit namespace packages for your directories. (A package is a module with submodules.) Ideally we'd configure Pytest with a path from which it would also generate this, but it doesn't seem to know how to do that.
The easiest solution here is simply to add empty __init__.py files to all of the subdirectories under src/; this will cause Pytest to import everything using package/module names that start with directory names under src/.
The question How do I Pytest a project using PEP 420 namespace packages? discusses other solutions to this.

import looks in the following directories to find a module:
The home directory of the program. This is the directory of your root script. When you are running pytest your home directory is where it is installed (/usr/local/bin probably). No matter that you are running it from your src directory because the location of your pytest determines your home directory. That is the reason why it doesn't find the modules.
PYTHONPATH. This is an environment variable. You can set it from the command line of your operating system. In Linux/Unix systems you can do this by executing: 'export PYTHONPATH=/your/custom/path' If you wanted Python to find your modules from the test directory you should include the src path in this variable.
The standard libraries directory. This is the directory where all your libraries are installed.
There is a less common option using a pth file.
sys.path is the result of combining the home directory, PYTHONPATH and the standard libraries directory. What you are doing, modifying sys.path is correct. It is something I do regularly. You could try using PYTHONPATH if you don't like messing with sys.path

If you include an __init__.py file inside your tests directory, then when the program is looking to set a home directory it will walk 'upwards' until it finds one that does not contain an init file. In this case src/.
From here you can import by saying :
from geom.region import *
you must also make sure that you have an init file in any other subdirectories, such as the other nested test directory

I was wondering what to do about this problem too. After reading this post, and playing around a bit, I figured out an elegant solution. I created a file called "test_setup.py" and put the following code in it:
import sys, os
sys.path.append(os.path.dirname(os.path.abspath(__file__)))
I put this file in the top-level directory (such as src). When pytest is run from the top-level directory, it will run all test files including this one since the file is prefixed with "test". There are no tests in the file, but it is still run since it begins with "test".
The code will append the current directory name of the test_setup.py file to the system path within the test environment. This will be done only once, so there are not a bunch of things added to the path.
Then, from within any test function, you can import modules relative to that top-level folder (such as import geom.region) and it knows where to find it since the src directory was added to the path.
If you want to run a single test file (such as test_util.py) instead of all the files, you would use:
pytest test_setup.py test\test_util.py
This runs both the test_setup and test_util code so that the test_setup code can still be used.

Are so late to answer that question but usining python 3.9 or 3.10 u just need to add __init__.py folder in tests folders.
When u add this file python interprets this folders as a module.
Wold be like this
src/
main.py
util.py
test/
__init__.py
test_util.py
geom/
vector.py
region.py
test/
__init__.py
test_vector.py
test_region.py
so u just run pytest.
Sorry my poor english

Not the best solution, but maybe the fastest one:
cd path/python_folder
python -m pytest python_file.py