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Import Jupyter (ne IPython) notebooks into tests and scripts.

Project description

importnb imports notebooks as modules. Notebooks are reusable as tests, source code, importable modules, and command line utilities.

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Installation
pip install importnb

conda install -c conda-forge importnb

importnb for testing

After importnb is installed, pytest will discover and import notebooks as tests.

pytest index.ipynb

importnb imports notebooks as python modules, it does not compare outputs like nbval.

importnb now captures doctests in every Markdown cell & block string expression. The docstrings are tested with the --doctest-modules flag.

pytest index.ipynb --doctest-modules

It is recommended to use importnb with --nbval.

pytest index.ipynb --nbval

importnb for the commmand line

importnb can run notebooks as command line scripts. Any literal variable in the notebook, may be applied as a parameter from the command line.

ipython -m importnb -- index.ipynb --foo "A new value"

importnb for Python and IPython

It is suggested to execute importnb-install to make sure that notebooks for each IPython session.

Restart and run all or it didn't happen.

importnb excels in an interactive environment and if a notebook will Restart and Run All then it may reused as python code. The Notebook context manager will allow notebooks with valid names to import with Python.

>>> from importnb import Notebook

For brevity

    with __import__('importnb').Notebook(): 
        import readme

importnb.loader will find notebooks available anywhere along the sys.path.

or explicity

    from importnb import Notebook
    with Notebook(): 
        import readme
    foo = 42
    import readme
    assert readme.foo is 42
    assert readme.__file__.endswith('.ipynb')

importnb readme

Modules may be reloaded

The context manager is required to reload a module.

    from importlib import reload
    with Notebook(): __name__ == '__main__' and reload(readme)

Lazy imports

The lazy option will delay the evaluation of a module until one of its attributes are accessed the first time.

    with Notebook(lazy=True):
        import readme

Fuzzy File Names

    if __name__ == '__main__':
        with Notebook():
            import __a_me

        assert __a_me.__file__ == readme.__file__

Python does not provide a way to import file names starting with numbers of contains special characters. importnb installs a fuzzy import logic to import files containing these edge cases.

import __2018__6_01_A_Blog_Post

will find the first file matching *2018*6?01?A?Blog?Post. Importing Untitled314519.ipynb could be supported with the query below.

import __314519

Docstring

The first markdown cell will become the module docstring.

    if __name__ == '__main__':
        print(readme.__doc__.splitlines()[0])
__importnb__ imports notebooks as modules.  Notebooks are reusable as tests, source code, importable modules, and command line utilities.

Meaning non-code blocks can be executeb by doctest.

    if __name__ == '__main__':
        __import__('doctest').testmod(readme)

Import notebooks from files

Notebook names may not be valid Python paths. In this case, use Notebook.from_filename.

   Notebook.from_filename('index.ipynb')

Import under the __main__ context.

   Notebook('__main__').from_filename('index.ipynb')

Parameterize Notebooks

Literal ast statements are converted to notebooks parameters.

In readme, foo is a parameter because it may be evaluated with ast.literal_val

    if __name__ == '__main__':
        from importnb import Parameterize
        f = Parameterize.load(readme.__file__)

The parameterized module is a callable that evaluates with different literal statements.

    if __name__ == '__main__': 
        assert callable(f)
        f.__signature__
assert f().foo == 42
assert f(foo='importnb').foo == 'importnb'

Run Notebooks from the command line

Run any notebook from the command line with importnb. Any parameterized expressions are available as parameters on the command line.

!ipython -m importnb -- index.ipynb --foo "The new value"

Integrations

IPython

IPython Extension

Avoid the use of the context manager using loading importnb as IPython extension.

%load_ext importnb

%unload_ext importnb will unload the extension.

Default Extension

importnb may allow notebooks to import by default with

!importnb-install

If you'd like to play with source code on binder then you must execute the command above. Toggle the markdown cell to a code cell and run it.

This extension will install a script into the default IPython profile startup that is called each time an IPython session is created.

Uninstall the extension with importnb-install.

Run a notebook as a module

When the default extension is loaded any notebook can be run from the command line. After the importnb extension is created notebooks can be execute from the command line.

ipython -m readme

In the command line context, __file__ == sys.arv[0] and __name__ == '__main__' .

See the deploy step in the travis build.

Parameterizable IPython commands

Installing the IPython extension allows notebooks to be computed from the command. The notebooks are parameterizable from the command line.

ipython -m readme -- --help

py.test

importnb installs a pytest plugin when it is setup. Any notebook obeying the py.test discovery conventions can be used in to pytest. This is great because notebooks are generally your first test.

!ipython -m pytest -- src 

Will find all the test notebooks and configurations as pytest would any Python file.

Setup

To package notebooks add recursive-include package_name *.ipynb

Developer

Format and test the Source Code

    if __name__ == '__main__':
        if globals().get('__file__', None) == __import__('sys').argv[0]:
            print(foo, __import__('sys').argv)
        else:
            from subprocess import call
            !ipython -m pytest
            """Formatting"""
            from pathlib import Path
            from importnb.utils.export import export
            root = 'src/importnb/notebooks/'
            for path in Path(root).rglob("""*.ipynb"""):                
                if 'checkpoint' not in str(path):
                    export(path, Path('src/importnb') / path.with_suffix('.py').relative_to(root))
            !jupyter nbconvert --to markdown --stdout index.ipynb > readme.md
    if __name__ == '__main__':
        try:
            from IPython.display import display, Image
            from IPython.utils.capture import capture_output
            from IPython import get_ipython
            with capture_output(): 
                get_ipython().system("cd docs && pyreverse importnb -opng -pimportnb")
            display(Image(url='docs/classes_importnb.png', ))
        except: ...

CHANGELOG

0.4.0

  • Fuzzy name completion.
  • A configurable extension system for magics.
  • Interactive(shell=False) is the default loader.

0.3.2

  • Add remote loader. Load notebooks from remote urls.
  • Support a fuzzy name import system. Files with special characters and numbers are importable.
  • An IPython magic to allow relative imports during interactive computing.

0.3.1

  • In loaders Notebook, Interactive, Execute, and Parameterize
  • Remove Partial, Lazy, and NotebookTest loaders.
  • The first Markdown cell imports as a docstrings, permitting doctests on markdown cells.
  • Notebook(globals={}) passes global values to the module
  • Notebook(dir="..") will change the working directory and path.
  • The code is pure python and uses IPython when possible.
  • ipython -m importnb nodebook.ipynb runs a notebook.

0.2.9

  • Include Partial, Lazy, and NotebookTest loaders.
  • Transform markdown cells to literate block strings so they are included in the ast.
    • __doc__'s are extracted from the first markdown cell or normal source code from a code cell.
  • Export the python source code with black.
  • Notebook.from_filename is a loader for paths and strings.
  • Add importnb.nbtest for notebook testing tools..
  • Benchmark importnb against existing notebooks.
  • Include a watchdog trick to watch tests..
  • Extend the project to >= 3.4
  • Use nbviewer/github hierachy for the docs.

0.2.4

  • Use tox for testing
  • Use a source directory folder structure for pytest and tox testing.
  • Create a pytest plugin that discovers notebooks as tests. With importnb notebooks can be used as fixtures in pytest.
  • Install importnb as an IPython extension.
  • Support running notebooks as modules from the ipython command line
  • Create a setuptools command to allow notebooks as packages.

0.2.1

  • importnb supports notebook inputs from pure python environments. Two compatible compiler were created from IPython and Python

  • importnb.Partial works appropriately by improving exceptions.

  • All of the IPython magic syntaxes were removed to support Pure Python.

  • The generated Python files are formatted with black.

  • Tests were added to:

    • Validate the line number in tracebacks
    • Test someone elses notebooks

0.1.4

  • Pypi supports markdown long_description with the proper mimetype in long_description_content_type.

0.1.3

  • Include the RST files in the MANIFEST.in.

0.1.2 (Unreleased)

  • Use RST files to improve the literacy of the pypi description.

0.1.1

  • Released on PyPi

0.0.2

  • Initial Testing Release

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