GitHub - scientific-python/pytest-doctestplus: Pytest plugin providing advanced doctest features (original) (raw)

pytest-doctestplus

Zenodo DOI CI Status

This package contains a plugin for the pytest framework that provides advanced doctest support and enables the testing of various text files, such as reStructuredText (".rst"), markdown (".md"), and TeX (".tex").

Motivation

This plugin provides advanced features for testing example Python code that is included in Python docstrings and in standalone documentation files.

Good documentation for developers contains example code. This is true of both standalone documentation and of documentation that is integrated with the code itself. Python provides a mechanism for testing code snippets that are provided in Python docstrings. The unit test framework pytest provides a mechanism for running doctests against both docstrings in source code and in standalone documentation files.

This plugin augments the functionality provided by Python and pytest by providing the following features:

Further, pytest-doctestplus supports editing files to fix incorrect docstrings (See Fixing Existing Docstrings).

Installation

The pytest-doctestplus plugin can be installed using pip:

$ pip install pytest-doctestplus

It is also possible to install the latest development version from the source repository:

$ git clone https://github.com/scientific-python/pytest-doctestplus $ cd pytest-doctestplus $ pip install .

In either case, the plugin will automatically be registered for use withpytest.

Usage

Note: In lieu of setup.cfg, pyproject.toml configuration is also supported; where setup.cfg is mentioned below, replace the syntax with TOML equivalent.

Setup and Configuration

This plugin provides three command line options: --doctest-plus for enabling the advanced features mentioned above, --doctest-rst for including*.rst files in doctest collection, and --doctest-ufunc for including doctests in docstrings of Numpy ufuncs.

This plugin can also be enabled by default by adding doctest_plus = enabledto the [tool:pytest] section of the package's setup.cfg file.

The plugin is applied to all directories and files that pytest collects. This means that configuring testpaths and norecursedirs insetup.cfg also affects the files that will be discovered bypytest-doctestplus. In addition, this plugin provides adoctest_norecursedirs configuration variable that indicates directories that should be ignored by pytest-doctestplus but do not need to be ignored by other pytest features.

Using pytest's built-in --doctest-modules option will override the behavior of this plugin, even if doctest_plus = enabled in setup.cfg, and will cause the default doctest plugin to be used. However, if for some reason both --doctest-modules and --doctest-plus are given, thepytest-doctestplus plugin will be used, regardless of the contents ofsetup.cfg.

pytest-doctestplus respects the --doctest-continue-on-failure flag. If set, doctests will report all failing lines, which may be useful to detect independent errors within the same doctest. However, it is likely to generate false positives when an early failure causes a variable later lines access to remain unset or have an unexpected value.

This plugin respects the doctest options that are used by the built-in doctest plugin and are set in doctest_optionflags in setup.cfg. By default,ELLIPSIS and NORMALIZE_WHITESPACE are used. For a description of all doctest settings, see the doctest documentation.

Running Tests in Markdown Files

To run doctests in Markdown files, invoke pytest with the command line options--doctest-plus --doctest-glob '*.md'.

If you write doctests inside GitHub-style triple backtick fenced code blocks, then in order for pytest-doctest to find and run them you need to include an extra trailing newline inside your code blocks, like this:

>>> 1 + 2
2

Doctest Directives

The pytest-doctestplus plugin defines doctest directives that are used to control the behavior of particular features. For general information on directives and how they are used, consult the documentation. The specifics of the directives that this plugin defines are described in the sections below.

Sphinx Doctest Directives

You can use testsetup and testcleanup in Sphinx RST to run code that is not visible in rendered document. However, due to how pytest-doctestplusworks, the code within needs to be prepended by >>>. For example:

.. testsetup::

>>> x = 42

.. testcleanup::

>>> del x

Floating Point Comparison

Some doctests may produce output that contains string representations of floating point values. Floating point representations are often not exact and contain roundoffs in their least significant digits. Depending on the platform the tests are being run on (different Python versions, different OS, etc.) the exact number of digits shown can differ. Because doctests work by comparing strings this can cause such tests to fail.

To address this issue, the pytest-doctestplus plugin provides support for aFLOAT_CMP flag that can be used with doctests. For example:

1.0 / 3.0 # doctest: +FLOAT_CMP 0.333333333333333311

{'a': 1 / 3., 'b': 2 / 3.} # doctest: +FLOAT_CMP {'a': 0.333333, 'b': 0.666666}

When this flag is used, the expected and actual outputs are both parsed to find any floating point values in the strings. Those are then converted to actual Python float objects and compared numerically. This means that small differences in representation of roundoff digits will be ignored by the doctest. The values are otherwise compared exactly, so more significant (albeit possibly small) differences will still be caught by these tests.

This flag can be enabled globally by adding it to setup.cfg as in

doctest_optionflags = NORMALIZE_WHITESPACE ELLIPSIS FLOAT_CMP

Ignoring warnings

If code in a doctest emits a warning and you want to make sure that warning is silenced, you can make use of the IGNORE_WARNINGS flag. For example:

import numpy as np np.mean([]) # doctest: +IGNORE_WARNINGS np.nan

Showing warnings

If code in a doctest emits a warning and you want to make sure that warning is shown, you can make use of the SHOW_WARNINGS flag. This is useful when warnings are turned into errors by pytest, and also because by default warnings are printed to stderr. This is the opposite from IGNORE_WARNINGS so obviously the two flags should not be used together. For example:

import numpy as np np.mean([]) # doctest: +SHOW_WARNINGS RuntimeWarning: Mean of empty slice. RuntimeWarning: invalid value encountered in double_scalars np.nan

Skipping Tests

Doctest provides the +SKIP directive for skipping statements that should not be executed when testing documentation.

open('file.txt') # doctest: +SKIP

In Sphinx .rst documentation, whole code example blocks can be skipped with the directive

.. doctest-skip::

>>> import asdf
>>> asdf.open('file.asdf')

However, it is often useful to be able to skip docstrings associated with particular functions, methods, classes, or even entire files.

Skipping All the Tests

It is also possible to skip all doctests below a certain line using a doctest-skip-all comment. Note the lack of :: at the end of the line here.

.. doctest-skip-all

import non_existing non_existing.write_pseudo_code() All the doctests are skipped in the file below

Skip Unconditionally

The pytest-doctestplus plugin provides a way to indicate that certain docstrings should be skipped altogether. This is configured by defining the variable __doctest_skip__ in each module where tests should be skipped. The value of __doctest_skip__ should be a list of wildcard patterns for all functions/classes whose doctests should be skipped. For example:

doctest_skip = ['myfunction', 'MyClass', 'MyClass.*']

skips the doctests in a function called myfunction, the doctest for a class called MyClass, and all methods of MyClass.

Module docstrings may contain doctests as well. To skip the module-level doctests:

doctest_skip = ['.', 'myfunction', 'MyClass']

To skip all doctests in a module:

doctest_skip = ['*']

Doctest Dependencies

It is also possible to skip certain doctests depending on whether particular dependencies are available. This is configured by defining the variable__doctest_requires__ at the module level. The value of this variable is a dictionary that indicates the modules that are required to run the doctests associated with particular functions, classes, and methods.

The keys in the dictionary are wildcard patterns like those described above, or tuples of wildcard patterns, indicating which docstrings should be skipped. The values in the dictionary are lists of module names that are required in order for the given doctests to be executed.

Consider the following example:

doctest_requires = {('func1', 'func2'): ['scipy']}

Having this module-level variable will require scipy to be importable in order to run the doctests for functions func1 and func2 in that module.

Similarly, in Sphinx .rst documentation, whole code example blocks can be conditionally skipped if a dependency is not available.

.. doctest-requires:: asdf

>>> import asdf
>>> asdf.open('file.asdf')

Furthermore, if the code only runs for specific versions of the optional dependency, you can add a version check like this:

.. doctest-requires:: asdf<3

>>> import asdf
>>> asdf.open('file.asdf')

Finally, it is possible to skip collecting doctests in entire subpackages by using the doctest_subpackage_requires in the [tool:pytest] section of the package's setup.cfg file. The syntax for this option is a list ofpath = requirements, e.g.:

doctest_subpackage_requires = astropy/wcs/* = scipy>2.0;numpy>1.14 astropy/cosmology/* = scipy>1.0

Multiple requirements can be specified if separated by semicolons.

It is also possible to conditionally skip all the doctests in a narrative documentation with doctest-requires-all.

Remote Data

The pytest-doctestplus plugin can be used in conjunction with thepytest-remotedata plugin in order to control doctest code that requires access to data from the internet. In order to make use of these features, thepytest-remotedata plugin must be installed, and remote data access must be enabled using the --remote-data command line option to pytest. See the pytest-remotedata plugin documentation for more details.

The following example illustrates how a doctest that uses remote data should be marked:

from urlib.request import urlopen url = urlopen('http://astropy.org') # doctest: +REMOTE_DATA

The +REMOTE_DATA directive indicates that the marked statement should only be executed if the --remote-data option is given. By default, all statements marked with the remote data directive will be skipped.

Whole code example blocks can also be marked to control access to data from the internet this way:

.. doctest-remote-data::

>>> import requests
>>> r = requests.get('https://www.astropy.org')

Sphinx Compatibility

To use the additional directives when building your documentation with sphinx you may want to enable the sphinx extension which registers these directives with sphinx. Doing so ensures that sphinx correctly ignores these directives, running the doctests with sphinx is not supported. To do this, add'pytest_doctestplus.sphinx.doctestplus' to your extensions list in yourconf.py file.

Fixing Existing Docstrings

The plugin has basic support to fix docstrings, this can be enabled by running pytest with --doctest-plus-generate-diff. Without further options, this will print out a diff and a list of files that would be modified. Using --doctest-plus-generate-diff=overwrite will modify the files in-place, so it is recommended to run the check first to verify the paths. You may wish to review changes manually and only commit some patches e.g. using git commit --patch.

The current diff generation is still very basic, for example, it does not account for existing .... By default a diff is only generated for failing doctests.

In general, a mass edit may wish to focus on a specific change and possibly include passing tests. So you can opt-in into the behavior by adding a hook to your conftest.py:

@pytest.hookimpl def pytest_doctestplus_diffhook(info): info["use"] = True # Overwrite all results (even successes) if info["fileno"] is None: # E.g. NumPy has C docstrings that cannot be found, we can add # custom logic here to try and find these: info["filename"] = ... info["lineno"] = ...

Where info is a dictionary containing the following items:

You can modify the dictionary in-place to modify the behavior.

Please note that we assume that this API will be used only occasionally and reserve the right to change it at any time.

Development Status

Questions, bug reports, and feature requests can be submitted on github.

License

This plugin is licensed under a 3-clause BSD style license - see theLICENSE.rst file.