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ouseful-PR / nbval

A py.test plugin to validate Jupyter notebooks
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Py.test plugin for validating Jupyter notebooks

Tests PyPI Version Documentation Status

The plugin adds functionality to py.test to recognise and collect Jupyter notebooks. The intended purpose of the tests is to determine whether execution of the stored inputs match the stored outputs of the .ipynb file. Whilst also ensuring that the notebooks are running without errors.

The tests were designed to ensure that Jupyter notebooks (especially those for reference and documentation), are executing consistently.

Each cell is taken as a test, a cell that doesn't reproduce the expected output will fail.

See docs/source/index.ipynb for the full documentation.

This Fork (ouseful-PR/nbval@table-test)

Example usage: py.test --nbval --nbval-skip-timeit --nbval-skip-memit Part\ 05*

We can ignore a notebook for testing purposes by setting "nbval_nb_ignore": true in notebook metadata.

This fork currently recognises the following additional tags to the tags provided by nbval (nbval-skip, nbval-ignore-output, nbval-raises-exception)):

The command line switches --nbval-skip-timeit and --nbval-skip-memit can be used to skip lines run with %timeit or %memit line magics (the line is commented out; commands over multiple lines will error...). An nbval-run-all tag can be added to a cell to prevent a magicked line being commented out (if for example we need the line to write a file...)

The cell tags provide a way of weakening test equivalence in a way that still allows useful tests to be performed. This is particularly useful where instructional notebooks are being tested that do not return strictly reproducible cell outputs, but where the shape or type of the returned elements from a particular cell should be consistent.

These tests are being developed as part of an ongoing process to support the use and deployment of notebook based teaching materials over several years of course presentation in a distance education context. The notebooks themselves are intended to remain largely unchanged over time, but the Docker container based environment is updated on a per course presentation basis. Previously run notebooks are automatically tested in updated Docker containers to ensure that outputs are consistent with previous runs, if not strictly identical to them. Warnings and errors arising from updates will also be captured.

A regular expression sanitiser can also be used to reduce the number of cell run failures by rewriting conventionally variable content.

Useful Sanitiser Regular Expressions

NB sanitiser code is embedded in this forked version of nbval.

The first line is IPython magic that would write the remaining contents to the specified file. Omit that first line if you are copying and pasting the regexes for your own sanitiser file.

%%writefile ouseful-sanitiser.cfg
[regex1]
regex: Figure size \d.*x\d.*
replace: FIGURE-SIZE
[regex2]
regex: .* per loop (mean ± std. dev. of \d+ runs, \d+ loops? each)
replace: TIMING-REPORT
[regex3]
regex: peak memory: .* MiB, increment: .* MiB
replace: MEMORY-REPORT
[regex4]
regex: File size \(.*\): .*B
replace: FILE_SIZE
[regex5]
regex: <pymongo.results.InsertOneResult at.*>
replace: <pymongo.results.InsertOneResult>
[regex6]
regex: ObjectId\('.*'\)
replace: ObjectId(...)
[regex7]
regex: <pymongo.results.UpdateResult at .*>
replace: <pymongo.results.UpdateResult>
[regex8]
regex: <pymongo.results.InsertManyResult at .*>
replace: <pymongo.results.InsertManyResult>
[regex9]
regex: 0x[0-9a-f]*
replace: 0xHASH
[regex10]
regex: <Graph identifier=.* \(<class 'rdflib.graph.Graph'>\)>
replace: <Graph identifier=IDENTIFER (<class 'rdflib.graph.Graph'>)>

We can use the sanitiser file with a command of the form py.test --nbval */*.ipynb --sanitize-with ouseful-sanitiser.cfg

Installation

Install this branch:

pip install --upgrade git+https://github.com/ouseful-PR/nbval.git@table-test

Original / official package available on PyPi:

pip install nbval

or install the latest version from cloning the repository and running:

pip install .

from the main directory. To uninstall:

pip uninstall nbval

For HTML reports, also install:

pip install pytest-html

How it works

The extension looks through every cell that contains code in an IPython notebook and then the py.test system compares the outputs stored in the notebook with the outputs of the cells when they are executed. Thus, the notebook itself is used as a testing function. The output lines when executing the notebook can be sanitized passing an extra option and file, when calling the py.test command. This file is a usual configuration file for the ConfigParser library.

Regarding the execution, roughly, the script initiates an IPython Kernel with a shell and an iopub sockets. The shell is needed to execute the cells in the notebook (it sends requests to the Kernel) and the iopub provides an interface to get the messages from the outputs. The contents of the messages obtained from the Kernel are organised in dictionaries with different information, such as time stamps of executions, cell data types, cell types, the status of the Kernel, username, etc.

In general, the functionality of the IPython notebook system is quite complex, but a detailed explanation of the messages and how the system works, can be found here

https://jupyter-client.readthedocs.io/en/latest/messaging.html#messaging

Execution

To execute this plugin, you need to execute py.test with the nbval flag to differentiate the testing from the usual python files:

py.test --nbval

To generate an HTML report (requires pytest-html), add the following to the command:

--html=report.html --self-contained-html

You can also specify --nbval-lax, which runs notebooks and checks for errors, but only compares the outputs of cells with a #NBVAL_CHECK_OUTPUT marker comment.

py.test --nbval-lax

The commands above will execute all the .ipynb files and 'pytest' tests in the current folder. Specify -p no:python if you would like to execute notebooks only. Alternatively, you can execute a specific notebook:

py.test --nbval my_notebook.ipynb

To check numbered notebooks:

py.test --nbval Part\ 01*/[[:digit:]]*.ipynb

By default, each .ipynb file will be executed using the kernel specified in its metadata. You can override this behavior by passing either --nbval-kernel-name mykernel to run all the notebooks using mykernel, or --current-env to use a kernel in the same environment in which pytest itself was launched.

If the output lines are going to be sanitized, an extra flag, --nbval-sanitize-with together with the path to a confguration file with regex expressions, must be passed, i.e.

py.test --nbval my_notebook.ipynb --nbval-sanitize-with path/to/my_sanitize_file

where my_sanitize_file has the following structure.

[Section1]
regex: [a-z]*
replace: abcd

regex: [1-9]*
replace: 0000

[Section2]
regex: foo
replace: bar

The regex option contains the expression that is going to be matched in the outputs, and replace is the string that will replace the regex match. Currently, the section names do not have any meaning or influence in the testing system, it will take all the sections and replace the corresponding options.

Coverage

To use notebooks to generate coverage for imported code, use the pytest-cov plugin. nbval should automatically detect the relevant options and configure itself with it.

Parallel execution

nbval is compatible with the pytest-xdist plugin for parallel running of tests. It does however require the use of the --dist loadscope flag to ensure that all cells of one notebook are run on the same kernel.

Documentation

The narrative documentation for nbval can be found at https://nbval.readthedocs.io.

Help

The py.test system help can be obtained with py.test -h, which will show all the flags that can be passed to the command, such as the verbose -v option. Nbval's options can be found under the Jupyter Notebook validation section.

Acknowledgements

This plugin was inspired by Andrea Zonca's py.test plugin for collecting unit tests in the IPython notebooks (https://github.com/zonca/pytest-ipynb).

The original prototype was based on the template in https://gist.github.com/timo/2621679 and the code of a testing system for notebooks https://gist.github.com/minrk/2620735 which we integrated and mixed with the py.test system.

We acknowledge financial support from

Authors

2014 - 2017 David Cortes-Ortuno, Oliver Laslett, T. Kluyver, Vidar Fauske, Maximilian Albert, MinRK, Ondrej Hovorka, Hans Fangohr