Run notebooks from another notebook, with input parameters

notebook_runner.py

def run_notebook(notebook_name):
    """Runs the notebook `notebook_name` (file name with no extension).

    This function executes notebook with name `notebook_name` (no extension)
    and saves the fully executed notebook in a new file appending "-out"
    to the original file name.

    It also displays links to the original and executed notebooks.
    """
    nb_name_full  = notebook_name + '.ipynb'
    display(FileLink(nb_name_full))
    
    out_path = 'out_notebooks/'
    out_nb_name = out_path + notebook_name + '-out.ipynb'
    
    nb = nbformat.read(nb_name_full, as_version=4)
    ep = ExecutePreprocessor(timeout = 3600)

    try:
        out = ep.preprocess(nb, {'metadata': {'path': './'}})
    except Exception:
        msg = 'Error executing the notebook "%s".\n\n' % notebook_name
        msg += 'See notebook "%s" for the traceback.' % out_nb_name
        print(msg)
        raise
    finally:
        nbformat.write(nb, out_nb_name)
        display(FileLink(out_nb_name))
    

def run_notebook_template(notebook_name, remove_out=True,
                          data_ids=['7d', '12d', '17d', '22d', '27d'],
                          ph_sel=None):
    """Run a template ALEX notebook for all the 5 samples.

    Fit results are saved in the folder 'results'.
    For each sample, the evaluated notebook containing both plots
    and text output is saved in the 'out_notebooks' folder.
    """
    ## Compute TXT data results file name (removing a previous copy)
    assert ph_sel in ['all-ph', 'Dex', 'DexDem', 'AexAem', 'AND-gate', None]
    ph_sel_suffix = '' if ph_sel is None else '-%s' % ph_sel
    data_fname = 'results/' + notebook_name + '%s.txt' % ph_sel_suffix
    if remove_out and \
       os.path.exists(data_fname):
            os.remove(data_fname)

    nb_name_full = notebook_name + '.ipynb'
    display(FileLink(nb_name_full))

    out_path = 'out_notebooks/'
    
    ep = ExecutePreprocessor(timeout = 3600)
    for data_id in data_ids:
        nb = nbformat.read(nb_name_full, as_version=4)
        
        nb['cells'].insert(1, nbformat.v4.new_code_cell('data_id = "%s"' % data_id))
        nb['cells'].insert(1, nbformat.v4.new_code_cell('ph_sel_name = "%s"' % ph_sel))

        out_nb_name = out_path + notebook_name + '-out%s-%s.ipynb' %\
                      (ph_sel_suffix, data_id)
    
        try:
            out = ep.preprocess(nb, {'metadata': {'path': './'}})
        except:
            msg = 'Error executing the notebook "%s".\n\n' % notebook_name
            msg += 'See notebook "%s" for the traceback.' % out_nb_name
            print(msg)
            raise
        finally:
            nbformat.write(nb, out_nb_name)
            display(FileLink(out_nb_name))
    display(pd.read_csv(data_fname, sep="\s+").set_index('sample'))