Python package structure information#
-This section provides guidance on your Python package’s structure, code formats -and style. It also reviews the various packaging tools that you can use to -support building and publishing your package.
+Python Package Structure#
+This section provides guidance on your Python package’s structure, code format, +and style. It also reviews the various packaging tools you can use to +build and publish your Python package.
+If you want end-to-end tutorials, check out our tutorial series that starts by introducing what a Python package is.
If you are confused by Python packaging, you are not alone! The good news is -there are some great modern packaging tools that ensure that you’re following -best practices. Here, we review tool features and suggest tools that might be -best fitted for your workflow.
+that some great modern packaging tools ensure you follow +best practices. Here, we review tool features and suggest tools you can use +for your Python packaging workflow. +Checkout our beginning-to-end create a Python package tutorials
+
+
How this content is developed
+All of the content in this guide has been vetted by community members, including maintainers and developers of the core packaging tools.
+
diff --git a/package-structure-code/publish-python-package-pypi-conda.html b/package-structure-code/publish-python-package-pypi-conda.html
index 71a10d09..941a2b57 100644
--- a/package-structure-code/publish-python-package-pypi-conda.html
+++ b/package-structure-code/publish-python-package-pypi-conda.html
@@ -464,7 +464,7 @@
- Python package structure information
+ Python Package Structure
Publishing Your Package In A Community Repository: PyPI or Anaconda.org
diff --git a/package-structure-code/pyproject-toml-python-package-metadata.html b/package-structure-code/pyproject-toml-python-package-metadata.html
index d70f7c31..a7b5964d 100644
--- a/package-structure-code/pyproject-toml-python-package-metadata.html
+++ b/package-structure-code/pyproject-toml-python-package-metadata.html
@@ -464,7 +464,7 @@
- Python package structure information
+ Python Package Structure
Use a pyproject.toml file for your package configuration & metadata
diff --git a/package-structure-code/python-package-build-tools.html b/package-structure-code/python-package-build-tools.html
index 7a2daba8..44c2a35a 100644
--- a/package-structure-code/python-package-build-tools.html
+++ b/package-structure-code/python-package-build-tools.html
@@ -464,7 +464,7 @@
- Python package structure information
+ Python Package Structure
Python Packaging Tools
diff --git a/package-structure-code/python-package-distribution-files-sdist-wheel.html b/package-structure-code/python-package-distribution-files-sdist-wheel.html
index 335a22df..75f032ad 100644
--- a/package-structure-code/python-package-distribution-files-sdist-wheel.html
+++ b/package-structure-code/python-package-distribution-files-sdist-wheel.html
@@ -464,7 +464,7 @@
- Python package structure information
+ Python Package Structure
Learn about Building a Python Package
@@ -623,8 +623,8 @@
-How to create the distribution format that PyPI and Pip expects?You can learn more about conda builds here.
Source Distribution (sdist)#
+What is a source distribution (sdist)#
Source files are the unbuilt files needed to build your package. These are the “raw / as-is” files that you store on GitHub or whatever platform you use to manage your code.
@@ -690,8 +690,8 @@How to create the distribution format that PyPI and Pip expects?
-Wheel (.whl files):#
+
+What is a Python wheel (whl):#
A wheel file is a ZIP-format archive whose filename follows a specific format
(below) and has the extension .whl. The .whl archive contains a specific
set of files, including metadata that are generated from your project’s
@@ -816,8 +816,8 @@
How to create the distribution format that PyPI and Pip expects?How to create the distribution format that PyPI and Pip expects?
-
Source Distribution (sdist)
-Wheel (.whl files):
+What is a source distribution (sdist)
+What is a Python wheel (whl):
What is a Python wheel (whl):#
A wheel file is a ZIP-format archive whose filename follows a specific format
(below) and has the extension .whl. The .whl archive contains a specific
set of files, including metadata that are generated from your project’s
@@ -816,8 +816,8 @@
How to create the distribution format that PyPI and Pip expects?How to create the distribution format that PyPI and Pip expects? -
Python Package Structure for Scientific Python Projects#
There are two different layouts that you will commonly see within the Python packaging ecosystem: -src and flat layouts. +src and flat layouts. Both layouts have advantages for different groups of maintainers.
We strongly suggest, but do not require, that you use the src/ layout (discussed below) for creating your Python package. This layout is also recommended in the -PyPA packaging guide.
+PyPA packaging guide tutorial.pyOpenSci will never require a specific package structure for peer review
-We understand that it would be tremendous effort for existing +
We understand that it would take significant effort for existing maintainers to move to a new layout.
The overview on this page presents recommendations that we think are best for someone getting started with Python packaging or someone who’s package has a simple build and might be open to moving to a more fail-proof approach.
+Other resources you can check out:
+An example of the src/package layout structure can be seen below.
+You can use tools like Hatch to quickly create a modern Python package structure. Check out our quickstart tutorial:
+Want to learn how to create the structure to build your package? Click here.
+What is the Python package source layout?#
+An example of the src/package layout structure is below.
myPackageRepoName
├── CHANGELOG.md ┐
├── CODE_OF_CONDUCT.md │
@@ -522,8 +530,8 @@ Python Package Structure for Scientific Python Projects
Note the location of the following directories in the example above:
-docs/: discussed in our docs chapter, this directory contains your user-facing documentation website. In a src/ layout docs/ are normally included at the same directory level of the src/ folder.
tests/ this directory contains the tests for your project code. In a src/ layout tests are normally included at the same directory level of the src/ folder.
docs/: Discussed in our docs chapter, this directory contains your user-facing documentation website. In a src/ layout docs/ are normally included at the same directory level as the src/ folder.
tests/ This directory contains the tests for your project code. In a src/ layout, tests are normally included at the same directory level as the src/ folder.
src/package/: this is the directory that contains the code for your Python project. “Package” is normally your project’s name.
Also in the above example, notice that all of the core documentation files that
@@ -537,8 +545,7 @@
Python Package Structure for Scientific Python ProjectsREADME.md
-Click here to read about our packaging documentation requirements.
-While we recommend the src/ layout we also review the flat layout here. Both are used in the Python ecosystem.
+Click here to read about our packaging documentation requirements.
Example scientific packages that use src/package layout
+
The src/ layout and testing#
-The benefit of using the src/package layout, particularly if you
-are creating a new package, is that it ensures tests are run against the
+
The benefit of using the src/package layout is that it ensures tests are run against the
installed version of your package rather than the files in your package
working directory. If you run your tests on your files rather than the
-installed version, you may be missing issues that users encounter when
+installed version of your package, you may be missing issues that users encounter when
your package is installed.
-If tests/ are outside of the src/package directory, they aren’t included in the package wheel. This makes your package size slightly smaller which then places places a smaller storage burden on PyPI which has over 400,000 packages to support.
+If tests/ are outside the src/package directory, they aren’t included in the package’s wheel. This makes your package size slightly smaller, which places a smaller storage burden on PyPI, and makes them faster to fetch.
@@ -565,76 +572,72 @@ The src/ layout and testingHow Python discovers and prioritizes importing modules
By default, Python adds a module in your current working directory to the front of the Python module search path.
This means that if you run your tests in your package’s working directory, using a flat layout, /package/module.py, Python will discover package/module.py file before it discovers the installed package.
-However, if your package lives in a src/ directory structure src/package then it won’t be, by default, added to the Python path. This means that when you import your package, Python will be forced to search the active environment (which has your package installed).
-Note: Python versions 3.11 and above have a path setting that can be adjusted to ensure the priority is to use installed packages first (e.g. PYTHONSAFEPATH).
+However, if your package lives in a src/ directory structure src/package, then it won’t be added to the Python path by default. This means that when you import your package, Python will be forced to search the active environment (which has your package installed).
+Note: Python versions 3.11 and above have a path setting that can be adjusted to ensure the priority is to use installed packages first (e.g., PYTHONSAFEPATH).
Sometimes tests are needed in a distribution#
-We do not recommend including tests as part of your package wheel by default. However, not including tests in your package distribution will make it harder for people other than yourself to test whether your package is functioning correctly on their system. If you have a small test suite (Python files + data), and think your users may want to run tests locally on their systems, you can include tests by moving the tests/ directory into the src/package directory (see example below).
Don’t include tests in your package wheel#
+Writing tests for your package is important; however, we do not recommend including tests as part of your package wheel by default. However, not including tests in your package distribution will make it harder for people other than yourself to test whether your package runs properly on their system. If you have a small test suite (Python files + data), and think your users may want to run tests locally on their systems, you can include tests by moving the tests/ directory into the src/package directory (see example below).
src/
package/
tests/
docs/
Including the tests/ directory in your src/package directory ensures that tests will be included in your package’s wheel.
+Including the tests/ directory in your src/package directory ensures that tests will be included in your package’s wheel.
Be sure to read the pytest documentation for more about including tests in your package distribution.
Challenges with including tests and data in a package wheel
-Tests, especially when accompanied by test data can create a few small challenges including:
+Tests, especially when accompanied by test data, can create a few small challenges, including:
-
-
Take up space in your distribution which will build up over time as storage space on PyPI
-Large file sizes can also slow down package install.
+Take up space in your distribution, which will build up over time as storage space on PyPI
+Large file sizes can also slow down package installation.
However, in some cases, particularly in the scientific Python ecosystems you may need to include tests.
+However, in some cases, particularly in the scientific Python ecosystem, you may need to include tests.
Don’t include test suite datasets in your package#
-If you do include your tests in your package distribution, we strongly +
If you include your tests in your package distribution, we strongly discourage you from including data in your test suite directory. Rather, host your test data in a repository such as Figshare or Zenodo. Use a tool such as Pooch to access the data when you (or a user) runs tests.
-Check out the testing section of our guide for more information about tests.
+For more information about Python package tests, see the tests section of our guide.
The src/package layout is semantically more clear. Code is always found in the src/package directory,
tests/anddocs/are in the root directory.
Important
-If your package tests require data, we suggest that you do NOT include that -data within your package structure. We will discuss this in more detail in a -tutorial. Include data in your package structure increases the size of your +
If your package tests require data, do NOT include that +data within your package structure. Including data in your package structure increases the size of your distribution files. This places a maintenance toll on repositories like PyPI and Anaconda.org that have to deal with thousands of package uploads.
+Click here for a quickstart tutorial on creating your Python package.
About the flat Python package layout#
-Currently most scientific packages use the flat-layout given:
+What is the flat Python package layout?#
+Many scientific packages use the flat-layout given:
-
-
It’s the most commonly found layout with the scientific Python ecosystem and -people tend to look to other packages / maintainers that they respect for examples -of how to build Python packages.
-Many Python tools depend upon tools in other language and / or complex builds -with compilation steps. Many developers thus appreciate / are used to features -of the flat layout.
+This layout is used by many core scientific Python packages such as NumPy, SciPy, and Matplotlib.
+Many Python tools depend upon tools in other languages and/or complex builds +with compilation steps. Many maintainers prefer features +of the flat layout for more complex builds.
While we present this layout here in our guide, we suggest that those just -getting started with python packaging start with the src/package layout -discussed above. Numerous packages in the ecosystem have had to move to a -src/ layout
+While we suggest that you use the src/package layout discussed above, it’s important to also +understand the flat layout, especially if you plan to contribute to a package that uses this layout.
Why most scientific Python packages do not use source
-In most cases the advantages of using the src/package layout for -larger scientific packages that already use flat approach are not worth it. -Moving from a flat layout to a src/package layout would come at a significant cost to -maintainers.
+In most cases, moving to the src/package layout for +larger scientific packages that already use a flat layout would consume significant time.
However, the advantages of using the src/package layout for a beginner are significant. -As such, we recommend that if you are getting started with creating a package, -that you consider using a src/package layout.
+As such, we recommend that you use the src/package layout if you are creating a new package. +Numerous packages in the ecosystem have had to move to a +src/package layout.
Benefits of using the flat layout in your Python package
Benefits of using the flat layout in your Python package
Benefits of using the flat layout in your Python package
+- What is the Python package source layout?
- The src/ layout and testing
-- About the flat Python package layout
+- What is the flat Python package layout?
- What does the flat layout structure look like?
diff --git a/package-structure-code/python-package-versions.html b/package-structure-code/python-package-versions.html
index 47d0d2d5..acfd536a 100644
--- a/package-structure-code/python-package-versions.html
+++ b/package-structure-code/python-package-versions.html
@@ -464,7 +464,7 @@
-
LICENSE & CODE_OF_CONDUCT to your Python package", "Add a README file to your Python package", "Command Line Reference Guide", "Get to Know Hatch", "Make your Python code installable", "Python packaging 101", "Publish your Python package that is on PyPI to conda-forge", "Publish your Python package to PyPI", "Make your Python package PyPI ready - pyproject.toml", "Using Hatch to Migrate setup.py to a pyproject.toml"], "titleterms": {"": [7, 14, 16, 23, 24, 38, 40, 42], "0": 36, "1": [7, 29, 36, 38, 39, 41, 42, 43], "101": 40, "2": [7, 29, 36, 38, 39, 41, 42, 43], "2fa": 42, "3": [29, 36, 38, 39, 41, 42, 43], "3b": 41, "4": [29, 36, 38, 39, 41, 42, 43], "5": [36, 39, 43], "6": [36, 39, 43], "7": 36, "8": 36, "A": [14, 19, 22, 24, 29], "For": 22, "If": [24, 42], "In": 24, "Of": 14, "That": 12, "The": [1, 9, 28, 36, 39, 40, 42], "__init__": 39, "about": [13, 19, 25, 26, 27, 28, 29, 39, 41, 42, 43], "accommod": 24, "account": 42, "across": 31, "action": 33, "ad": [16, 22, 41], "add": [22, 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\ No newline at end of file
diff --git a/tests/index.html b/tests/index.html
index 689cd6ca..b03e9f2a 100644
--- a/tests/index.html
+++ b/tests/index.html
@@ -11,12 +11,12 @@
-
+
-
+
Tests and data for your Python package#
+Tests and data for your Python package#
Tests are an important part of your Python package because they provide a set of checks that ensure that your package is functioning how you expect it to.
-In this section you will learn more about the importance of writing -tests for your Python package and how you can setup infrastructure +
In this section, you will learn more about the importance of writing +tests for your Python package and how you can set up infrastructure to run your tests both locally and on GitHub.
diff --git a/tutorials/intro.html b/tutorials/intro.html
index fe455f26..9c4aca4e 100644
--- a/tutorials/intro.html
+++ b/tutorials/intro.html
@@ -490,7 +490,7 @@
-Who are these tutorials for?
-
Python packaging 101#
+Python packaging 101#
A start to finish beginner-friendly tutorial
Welcome to the pyOpenSci Python packaging tutorial series. The lessons on the upcoming pages walk you through the core steps needed to @@ -534,7 +534,7 @@