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nb_runner

Jupyter notebook runner

From /dls_sw/i16/software/python/jupyter_processor/jproc.py

add_inpath(nb, filename)

Add inpath=filename to top of notebook

Source code in mmg_toolbox/utils/nb_runner.py 
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def add_inpath(nb: nbformat.NotebookNode, filename: str):
    """Add inpath=filename to top of notebook"""
    code = f"inpath = '{filename}'"
    first_cell = next(iter(nb.cells), {})
    first_cell_type = first_cell.get('cell_type', '')
    first_cell_source = first_cell.get('source', '')
    if first_cell_type == 'code' and 'inpath' in first_cell_source:
        # replace contents of cell
        first_cell['source'] = code
    else:
        # add a new cell
        add_code_cell(nb, code, index=0)

generate_notebook_html(nb)

Generate html of the notebook without running it return (html, resources)

Source code in mmg_toolbox/utils/nb_runner.py 
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def generate_notebook_html(nb: nbformat.NotebookNode) -> tuple[str, dict]:
    """
    Generate html of the notebook without running it
     return (html, resources)
    """
    html_exporter = HTMLExporter()
    return html_exporter.from_notebook_node(nb)

html_processor(nb)

Process notebook and return (html, resources)

Source code in mmg_toolbox/utils/nb_runner.py 
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def html_processor(nb: nbformat.NotebookNode) -> tuple[str, dict]:
    """
    Process notebook and return (html, resources)
    """
    processor = ExecutePreprocessor()
    html_exporter = HTMLExporter()
    print('\n'.join(str(cell) for cell in nb.cells))
    processor.preprocess(nb, resources={'metadata': {}})
    return html_exporter.from_notebook_node(nb)

process_template(template, nexus_filename, output_folder=None)

Process jupyter notebook

Source code in mmg_toolbox/utils/nb_runner.py 
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def process_template(template: str, nexus_filename: str, output_folder: str | None = None) -> tuple[str, str]:
    """
    Process jupyter notebook
    """
    nb = read_notebook(template)
    add_inpath(nb, nexus_filename)

    if output_folder is None:
        output_folder = TMPDIR
    out_name, ext = os.path.splitext(output_folder)
    if ext:
        out_html = out_name + '.html'
        out_pynb = out_name + '.ipynb'
    else:
        tmp_name, _ = os.path.splitext(os.path.basename(template))
        nxs_name, _ = os.path.splitext(os.path.basename(nexus_filename))
        out_name = f"{nxs_name}_{tmp_name}"
        out_html = os.path.join(output_folder, out_name + '.html')
        out_pynb = os.path.join(output_folder, out_name + '.ipynb')

    # run notebook
    (body, resources) = html_processor(nb)

    with open(out_html, 'w') as f:
        f.write(body)
    save_notebook(nb, out_pynb)
    print(f"Completed notebook, saved as: {out_pynb}")
    return out_pynb, out_html

reprocess_notebook(notebook_filename, output_folder=None)

Copy notebook and open jupyter for reprocessing of copied notebook in processing directory

Source code in mmg_toolbox/utils/nb_runner.py 
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def reprocess_notebook(notebook_filename: str, output_folder: str | None = None):
    """
    Copy notebook and open jupyter for reprocessing of copied notebook in processing directory
    """
    path, name = os.path.split(notebook_filename)

    if output_folder is None and path.endswith('/processed/notebooks'):
        output_folder = path.replace('/processed/notebooks', '/processing')

    if output_folder.endswith('.ipynb'):
        new_filename = output_folder
    else:
        new_filename = os.path.join(output_folder, name)

    if os.path.isfile(new_filename):
        print(f"{new_filename} already exists, it won't be overwritten")
    else:
        print(f"Creating {new_filename}")
        shutil.copy(notebook_filename, new_filename)
    run_jupyter_notebook(new_filename)

run_jupyter_notebook(notebook_filename)

Run a jupyter notebook

Source code in mmg_toolbox/utils/nb_runner.py 
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def run_jupyter_notebook(notebook_filename: str):
    """
    Run a jupyter notebook
    """
    command = f"jupyter notebook {notebook_filename}"
    run_command(command)

view_jupyter_notebook(notebook_filename)

Open a jupyter notebook.ipynb or .html file

Source code in mmg_toolbox/utils/nb_runner.py 
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def view_jupyter_notebook(notebook_filename: str):
    """
    Open a jupyter notebook.ipynb or .html file
    """
    if notebook_filename.endswith('.ipynb'):
        run_jupyter_notebook(notebook_filename)
    elif notebook_filename.endswith('.html'):
        webbrowser.open_new_tab(notebook_filename)

view_notebook_html(notebook_filename)

Convert a notebook to html and open it in a web-browser

Source code in mmg_toolbox/utils/nb_runner.py 
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def view_notebook_html(notebook_filename: str):
    """
    Convert a notebook to html and open it in a web-browser
    """
    out_html = os.path.join(TMPDIR, 'tmp_notebook.ipynb')
    nb = read_notebook(notebook_filename)
    (body, resources) = generate_notebook_html(nb)
    with open(out_html, 'w') as f:
        f.write(body)
    webbrowser.open_new_tab(notebook_filename)