Ultimate Setup For Your Next Python Project

24/1/2021 Ultimate Setup for Your Next Python Project | by Martin Heinz | Towards Data Science
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Ultimate Setup for Your Next Python Project

Starting any project from scratch can be a daunting task… But not if you have this
ultimate Python project blueprint!
Martin Heinz Jan 15, 2020 · 10 min read
Original image by @sxoxm on Unsplash
https://towardsdatascience.com/ultimate-setup-for-your-next-python-project-179bda8a7c2c 1/12
Whether you are working on some machine learning/AI project, building web apps in
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Flask or just writing some quick Python script, it’s always useful to have some template
for your project that satisfies all your needs, namely: predefined directory structure, all
necessary config files like pytest.ini or requirements.txt , Testing, linting and static
code analysis setup, CI/CD tooling, Dockerization of your app and on top of that
automation with Makefile. So, here I bring you exactly that in this "Ultimate" all-
purpose setup for your Python projects.
TL;DR: Here is my repository with full source code and docs:

https://github.com/MartinHeinz/python-project-blueprint
Directory Structure
When I was writing this kind of an article for Golang (here), I had a hard time figuring
out ideal project structure, with Python however, it’s pretty simple:
1 ├── blueprint # Our source code - name of the application/module

2 │ ├── app.py
3 │ ├── __init__.py
4 │ ├── __main__.py
5 │ └── resources
6 ├── tests
7 │ ├── conftest.py
8 │ ├── context.py
9 │ ├── __init__.py
10 │ └── test_app.py
11 ├── .github # GitHub Actions
12 │ └── workflows
13 │ ├── build-test.yml
14 │ └── push.yml
15 ├── Makefile
16 ├── configure_project.sh
17 ├── setup.cfg
18 ├── pytest.ini
19 ├── requirements.txt
20 ├── dev.Dockerfile
21 └── prod.Dockerfile
directory_tree.shell hosted with ❤ by GitHub view raw
Let’s outline what we have here, starting from the top:
blueprint - This is our source code directory, which should be named by your
application or package you are working on. Inside we have the usual __init__.py
file signifying that it's a Python package, next there is __main__.py which is used
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when we want to run our application directly with python -m blueprint . Last
source file here is the app.py which is here really just for demonstration purposes.
In real project instead of this app.py you would have few top level source files and
more directories (internal packages). We will get to contents of these files a little
later. Finally, we also have resources directory here, which is used for any static
content your application might need, e.g. images, keystore, etc.
tests - In this directory resides our test suite. I'm not gonna go into too much
detail here as we will dedicate whole section to testing, but just briefly:
1. test_app.py is a test file corresponding to app.py in source directory
2. conftest.py is probably familiar to you if you ever used Pytest - it's a file used for
specifying Pytest fixtures, hooks or loading external plugins.
3. context.py helps with imports of source code files from blueprint directory by
manipulating class path. We will see how that works in sec.
.github - This is the last directory we have in this project. It holds configurations
for GitHub Actions which we use for CI/CD. We have two files, first of them - build-
test.yml is responsible for building, testing and linting our source code on every
push. Second file - push.yml pushes our built application to GitHub Package
Registry every time we create tag/release on GitHub. More on this in a separate
blog post.
Makefile - Apart from directories, we also have a few top-level files in our project,
first of them - Makefile contains target that will help us automate commonly
performed tasks like building, testing, linting or cleaning our project
configure_project.sh - This one is a convenience script that sets up a project for

you. It essentially renames and substitutes dummy values in this project template
for real values like name of your project or name of your package. Pretty handy,
right?
Rest of the files we have here are configuration files for all tools we will use in this
project. Let’s jump over to the next section and explore what they do and what’s in
them.
Config Files
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One thing that can get pretty messy when setting up Python project is the config file
soup that you will end up with when you use a bunch of tools like, pylint, coverage.py,
flake8 and so on. Each of these tools would like to have its own file, usually something
like .flake8 or .coveragerc , which creates lots of unnecessary clutter in the root of
your project. To avoid this, I merged all these files into single one - setup.cfg :
1 [flake8]
2 exclude =
3 .git,
4 __pycache__,
5 .pytest_cache,
6 venv
7
8 ignore =
9 # Put Error/Style codes here e.g. H301
10
11 max-line-length = 120
12 max-complexity = 10
13
14 [bandit]
15 targets: blueprint
16
17 [coverage:run]
18 branch = True
19 omit =
20 */__main__.py
21 */tests/*
22 */venv/*
23
24 [coverage:report]
25 exclude_lines =
26 pragma: no cover
27 if __name__ == .__main__.:
28
29 [coverage:html]
30 directory = reports
31
32 [pylint]
33 ... # 100 lines of config...
setup.cfg hosted with ❤ by GitHub view raw
In case you are not familiar with all of the tools used here, I will give quick description:
Flake8 — is a tool for enforcing code style in your projects — in other words — it’s
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linter similar to pylint, which we will use as well. Why use both? It’s true that they
overlap, but both of them have some rules that the other doesn’t, so in my
experience it’s worth to use them both.
Bandit — is a tool for finding common security issues in Python code. It works by
creating AST (abstract syntax tree) from your code and running plugins against its
nodes. Developers are generally not security experts and also all of us make
mistakes here-and-there, so it’s always nice to have a tool that can spot at least
some of those security mistakes for us.
Coverage.py — is a tool for measuring code coverage of Python programs. It gets

triggered when we run our test suite with Pytest and generates coverage report
from the test run. These reports can be in the form of terminal output, but also
XML format which then can be consumed by CI tools.
With that out of the way, let’s go over what we have in setup.cfg . For Flake8 we define
exclusion patterns so that we don't lint code that we don't care about. Below that is an
empty ignore section in case we need to ignore some rule globally. We also set max
line length to 120, as keeping line length to 80 is in my opinion unreasonable with the
size of today's screens. Final line sets McCabe complexity threshold to 10, if you are not
familiar with cyclomatic complexity you can find out more here.
Next up is Bandit, all we configure here is target directory, which is the name of our
package. We do this so that we can avoid specifying targets on the command line.
After that follows Coverage.py. First, we enable branch coverage, which means that in
places where a line in your program could jump to more than one next line,
Coverage.py tracks which of those destination lines are actually visited. Next, we omit
some files that shouldn’t or can’t be included in coverage measurement, like tests
themselves or virtual environment files. We also exclude specific lines, e.g. lines that
are labeled with pragma: no cover comment. Last Coverage.py config line tells the tool
to store generated reports in reports directory. This directory is created automatically
if it doesn't exist already.
The final tool we need to configure is Pylint, the configuration though, is very
extensive, like more than 100 lines… So, I will leave this one out and point you the
source here as well as commented and explained pylintrc in Pylint repository here.
We went through all the tools in setup.cfg but there is one more that cannot be added
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to setup.cfg and that is Pytest - even though Pytest docs tell you that you can use
setup.cfg , it's not exactly true... As per this issue, the option to use setup.cfg is being
deprecated and there are some bugs like interpolation errors, that won't be fixed,
therefore we will also need pytest.ini file for configuration of Pytest:
1 [pytest]
2 addopts = --color=yes --cov=blueprint --cov-report=xml --cov-report=term -ra
3 filterwarnings =
4 log_cli = 1
5 log_cli_level = INFO
6 log_cli_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)
7 log_cli_date_format = %Y-%m-%d %H:%M:%S
pytest.ini hosted with ❤ by GitHub view raw
The first thing we do here is set a bunch of command line arguments — we enable
colors in terminal output, then we enable coverage reporting for blueprint directory,
after that we enable both generations of XML and stdout ( term ) coverage reports.
Final 2 arguments ( -ra ) tell Pytest to output short summary for non-passing tests.
On the next line, we have filterwarnings option which allows us to disable some
annoying warnings in the output, for example, deprecation warnings coming out of
some library which we have no control over.
Rest of the config sets up logging. First one just turns it on and other 3 configure level,
format and datetime format. Easier than explaining the format config is just seeing the
output itself, which is shown in the next section.
With all the configurations in pytest.ini , all we will need to do to run our test suite is
run pytest , not even the package argument needed!
Last actual configuration file we have is requirement.txt , which contains a list of our
dependencies. All you can find in this file is a list of Python packages, one per line with
the optional version of the package. As noted, the package version is optional, but I
strongly suggest you lock versions in requirements.txt to avoid situations, where you
might download newer, incompatible package during build and deployment, and end-
up breaking your application.
There are 2 remaining files which aren’t actually config files — our Dockerfiles, namely,
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dev.Dockerfile and prod.Dockerfile used for development and production images
respectively. I will leave those out for time being as we will explore those in a separate
article where we will talk about CI/CD and deployment. You can, however, check those
files out already in GitHub repository here - https://github.com/MartinHeinz/python-
project-blueprint/blob/master/dev.Dockerfile.
Actual Source Code

We have done quite a lot without even mentioning the source code of our application,
but I think it’s time to look at those few lines of code that are in the project skeleton:
1 # app.py
2 class Blueprint:
3
4 @staticmethod
5 def run():
6 print("Hello World...")
app.py hosted with ❤ by GitHub view raw
Only actual source code in this blueprint is this one class with a static method. This is
really on needed so that we can run something, get some output and test it. This also
works as entrypoint to the whole application. In a real project, you could use the run()
method to initialize your application or web server.
So, how do we actually run this piece of code?
1 # __main__.py
2 from .app import Blueprint
3
4 if __name__ == '__main__':
5 Blueprint.run()
__main__.py hosted with ❤ by GitHub view raw
This short snippet in a specially named file __main__.py is what we need in our project
so that we can run the whole package using python -m blueprint . The nice thing about
this file and it's contents is that it will only be run with that command, therefore if we
want to just import something from the source of this package without running the
whole thing, then we can do so without triggering Blueprint.run() .
There’s one more special file in our package and that’s the __init__.py file. Usually,
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you would leave it empty a use it only to tell Python that the directory is a package.
Here, however, we will use it to export classes, variables and functions from our
package.
1 # __init__.py
2 from .app import Blueprint
__init__.py hosted with ❤ by GitHub view raw
Without this one line above you wouldn’t be able to call Blueprint.run() from outside
of this package. This way we can avoid people using internal parts of our code that
should not be exposed.
That’s all for the code of our package, but what about the tests? First, let’s look at the
context.py
1 # context.py
2 import sys
3 import os
4 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
5
6 import blueprint # noqa # pylint: disable=unused-import, wrong-import-position
context.py hosted with ❤ by GitHub view raw
Normally when you use someone's package, then you import it like import blueprint
or from blueprint import Blueprint , to imitate this in our tests and therefore make it
as close as possible to real usage we use context.py file to import the package into our
test context. We also insert our project root directory into system path. This is not
actually necessary when running tests with pytest , but if you for example run
context.py directly with python ./tests/context.py or possibly with unittest
without including the sys.path.insert... , then you would get ModuleNotFoundError:
No module named 'blueprint' , so this one line is a little bit of insurance policy.
Now, let’s see the example test:
1 # test_app.py
2 from .context import blueprint
3
4
4
5 def test_app(capsys, example_fixture):
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6 # pylint: disable=W0612,W0613
7 blueprint.Blueprint.run()
8 captured = capsys.readouterr()
9
10 assert "Hello World..." in captured.out
test_app.py hosted with ❤ by GitHub view raw
What we have here is just a single test that checks the standard output of
Blueprint.run() using built-in Pytest fixture called capsys (capture system output).
So, what happens when we run the test suite?
1 ~ $ pytest
2 =========================================================== test session starts =======
3 collected 1 item
4
5 tests/test_app.py::test_app
6 -------------------------------------------------------------- live log setup ---------
7 2020-01-04 12:22:00 [ INFO] Setting Up Example Fixture... (conftest.py:9)
8 PASSED
9 ------------------------------------------------------------ live log teardown --------
10 2020-01-04 12:22:00 [ INFO] Tearing Down Example Fixture... (conftest.py:11)
11
12
13 ----------- coverage: platform linux, python 3.7.5-final-0 -----------
14 Name Stmts Miss Branch BrPart Cover
15 ---------------------------------------------------------
16 blueprint/__init__.py 1 0 0 0 100%
17 blueprint/app.py 3 0 0 0 100%
18 ---------------------------------------------------------
19 TOTAL 4 0 0 0 100%
20 Coverage XML written to file coverage.xml
pytest_run.console hosted with ❤ by GitHub view raw
I trimmed a few lines from the output so that you can better see the relevant parts of it.
What’s to note here? Well, our test passed! Other than that, we can see coverage report
and we can also see that the report got written to coverage.xml as configured in
pytest.ini . One more thing that we have here in the output is 2 log messages coming
from conftest.py . What is that about?
You might have noticed that apart from capsys fixture, we also used example_fixture
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in parameters of our small test. This fixture resides in conftest.py as should all custom
fixtures we make:
1 # conftest.py
2 import logging
3 import pytest
4
5 LOGGER = logging.getLogger(__name__)
6
7
8 @pytest.fixture(scope='function')
9 def example_fixture():
10 LOGGER.info("Setting Up Example Fixture...")
11 yield
12 LOGGER.info("Tearing Down Example Fixture...")
conftest.py hosted with ❤ by GitHub view raw
As the name implies, this really is just an example fixture. All it does is log one
message, then it lets the test run and finally, it logs one more message. The nice thing
about conftest.py file is that it gets automatically discovered by Pytest, so you don’t
even need to import it to your test files. If you want to find out more about it, then you
can check out my previous post about Pytest here or docs here.
One Command for Everything

It would be quite laborious if we were to run each of our tools separately and had to
remember their arguments, even though they are always the same. Also, it would be
equally annoying if later we decided to put all these tools into CI/CD (next article!),
right? So, let’s simplify things with Makefile :
In this Makefile we have 4 targets. First of them - run runs our application using
__main__.py we created in the root of our source folder. Next, test just runs pytest .
It's that simple thanks to all the configs in pytest.ini . The longest target here - lint -
runs all our linting tool. First, it runs pylint against all .py files in the project,
including test files. After that it runs flake8 and finally bandit . For these 2 it runs only
against sources in blueprint directory. If any of those tools find some problem with
our code, it will exit with non-zero code, meaning the target will fail, which will be
useful in CI/CD. Last target in this file is clean , which well... cleans our projects - it
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removes all the files generated by previously mentioned tools.
Conclusion
In this article we’ve built project skeleton, that’s ready to be used for any kind of Python
project you might be working on or thinking about, so if you want to play with or dig a
little deeper, then check out the source code which is available in my repository here:
https://github.com/MartinHeinz/python-project-blueprint. Repo also includes
information on how to set up your project using convenience script, plus some more
docs. Feel free to leave feedback/suggestions in the form of issue or just star it if you
like this kind of content. 🙂
In the future, we will look into adding CI/CD into the mix with GitHub Actions and
GitHub Package Registry. We will also Dockerize our project and create both
debuggable and optimized production ready Docker images and add some more code
quality tooling using CodeClimate and SonarCloud.
Resources
Sample Python Module Repository
Pytest Docs
Python Code Quality Authority
This article was originally posted at martinheinz.dev
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24/1/2021 Ultimate Setup for Your Next Python Project | by Martin Heinz | Towards Data Science

Follow 537K Followers

Martin Heinz Jan 15, 2020 · 10 min read

Original image by @sxoxm on Unsplash

TL;DR: Here is my repository with full source code and docs:

1 ├── blueprint # Our source code - name of the application/module

directory_tree.shell hosted with ❤ by GitHub view raw

Let’s outline what we have here, starting from the top:

1. test_app.py is a test file corresponding to app.py in source directory

configure_project.sh - This one is a convenience script that sets up a project for

setup.cfg hosted with ❤ by GitHub view raw

Coverage.py — is a tool for measuring code coverage of Python programs. It gets

pytest.ini hosted with ❤ by GitHub view raw

run pytest , not even the package argument needed!

Actual Source Code

app.py hosted with ❤ by GitHub view raw

method to initialize your application or web server.

So, how do we actually run this piece of code?

__main__.py hosted with ❤ by GitHub view raw

__init__.py hosted with ❤ by GitHub view raw

context.py hosted with ❤ by GitHub view raw

context.py directly with python ./tests/context.py or possibly with unittest

without including the sys.path.insert... , then you would get ModuleNotFoundError:

Now, let’s see the example test:

test_app.py hosted with ❤ by GitHub view raw

pytest_run.console hosted with ❤ by GitHub view raw

from conftest.py . What is that about?

conftest.py hosted with ❤ by GitHub view raw

One Command for Everything

Python Code Quality Authority

This article was originally posted at martinheinz.dev

Sign up for The Daily Pick

Emails will be sent to dirixev483@1adir.com.

Programming Software Development Technology Python Data Science

About Help Legal

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main.py hosted with ❤ by GitHub view raw

init.py hosted with ❤ by GitHub view raw