Python preprocessors.ExecutePreprocessor类代码示例

def test_tutorial_nb(file_path):
    """Run tutorial jupyter notebook to catch any execution error.

    Parameters
    ----------
    file_path : str
        path of tutorial markdown file
    """
    tutorial_name = os.path.basename(file_path)
    notebook = nbformat.read(file_path + '.ipynb', as_version=4)
    eprocessor = ExecutePreprocessor(timeout=1800)
    try:
        eprocessor.preprocess(notebook, {'metadata': {}})
    except Exception as err:
        err_msg = str(err)
        fail_dict[tutorial_name] = err_msg
    finally:
        output_nb = open("output.txt", mode='w')
        nbformat.write(notebook, output_nb)
        output_nb.close()
        output_nb = open("output.txt", mode='r')
        for line in output_nb:
            if "Warning:" in line:
                fail_dict[tutorial_name] = "%s has warning." % (tutorial_name)
                return

def _notebook_run(path):
    """Execute a notebook via nbconvert and collect output.
       :returns (parsed nb object, execution errors)
    """
    kernel_name = 'python%d' % sys.version_info[0]
    this_file_directory = os.path.dirname(__file__)
    errors = []
    with tempfile.NamedTemporaryFile(suffix=".ipynb", mode='wt') as fout:
        with open(path) as f:
            nb = nbformat.read(f, as_version=4)
            nb.metadata.get('kernelspec', {})['name'] = kernel_name
            ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=10)

            try:
                ep.preprocess(nb, {'metadata': {'path': this_file_directory}})
            except CellExecutionError as e:
                if "SKIP" in e.traceback:
                    print(str(e.traceback).split("\n")[-2])
                else:
                    raise e
            except RuntimeError as e:
                print(e)

            finally:
                nbformat.write(nb, fout)

    return nb, errors

def execute_nb(src, dst, allow_errors=False, timeout=1000, kernel_name=''):
    """
    Execute notebook in `src` and write the output to `dst`

    Parameters
    ----------
    src, dst: str
        path to notebook
    allow_errors: bool
    timeout: int
    kernel_name: str
        defualts to value set in notebook metadata

    Returns
    -------
    dst: str
    """
    import nbformat
    from nbconvert.preprocessors import ExecutePreprocessor

    with io.open(src, encoding='utf-8') as f:
        nb = nbformat.read(f, as_version=4)

    ep = ExecutePreprocessor(allow_errors=allow_errors,
                             timeout=timeout,
                             kernel_name=kernel_name)
    ep.preprocess(nb, resources={})

    with io.open(dst, 'wt', encoding='utf-8') as f:
        nbformat.write(nb, f)
    return dst

def main():
    arguments = docopt(__doc__, version='nbgen 2.0')

    cmd = subprocess.run([arguments["<path>"]] + arguments["<arguments>"], stdout=subprocess.PIPE)
    cmd.check_returncode()
    cells = json.loads(cmd.stdout.decode("utf-8"))

    nb_dict = {
      "metadata": {},
      "nbformat": 4,
      "nbformat_minor": 0,
      "cells": cells,
    }
    notebook = nbformat.from_dict(nb_dict)

    ep = ExecutePreprocessor(timeout=600, kernel_name='python3')
    ep.preprocess(notebook, {'metadata': {}})

    if arguments["nb"]:
        nbformat.write(notebook, "{}.ipynb".format(arguments["<name>"]))

    elif arguments["slides"]:
        config = Config()
        reveal_cdn = "https://cdnjs.cloudflare.com/ajax/libs/reveal.js/3.3.0/"
        config.SlidesExporter.reveal_url_prefix = (arguments["--reveal"] or reveal_cdn)

        slides, __ = export_slides(nb=notebook, config=config)
        with open("{}.html".format(arguments["<name>"]), "w") as html_file:
            html_file.write(slides)

    def _runTest(self):
        kernel = 'python%d' % sys.version_info[0]
        cur_dir = os.path.dirname(self.nbfile)

        with open(self.nbfile) as f:
            nb = nbformat.read(f, as_version=4)
            if self.cov:
                covdict = {'cell_type': 'code', 'execution_count': 1,
                           'metadata': {'collapsed': True}, 'outputs': [],
                           'nbsphinx': 'hidden',
                           'source': 'import coverage\n'
                                     'coverage.process_startup()\n'
                                     'import sys\n'
                                     'sys.path.append("{0}")\n'.format(cur_dir)
                           }
                nb['cells'].insert(0, nbformat.from_dict(covdict))

            exproc = ExecutePreprocessor(kernel_name=kernel, timeout=600)

            try:
                run_dir = os.getenv('WRADLIB_BUILD_DIR', cur_dir)
                exproc.preprocess(nb, {'metadata': {'path': run_dir}})
            except CellExecutionError as e:
                raise e

        if self.cov:
            nb['cells'].pop(0)

        with io.open(self.nbfile, 'wt') as f:
            nbformat.write(nb, f)

        self.assertTrue(True)

def execute_nb(src, dst, allow_errors=False, timeout=1000, kernel_name=None):
    '''
    Execute notebook in `src` and write the output to `dst`

    Parameters
    ----------
    src, dst: str
        path to notebook
    allow_errors: bool
    timeout: int
    kernel_name: str
        defualts to value set in notebook metadata

    Returns
    -------
    dst: str
    '''
    with io.open(src, encoding='utf-8') as f:
        nb = nbformat.read(f, as_version=4)

    ep = ExecutePreprocessor(allow_errors=False,
                             timeout=timeout,
                             kernel_name=kernel_name)
    ep.preprocess(nb, {'metadata': {'path': SOURCE_DIR}})

    with io.open(dst, 'wt', encoding='utf-8') as f:
        nbformat.write(nb, f)
    return dst

def run_notebook(notebook_name, nb_kwargs=None,
                 insert_pos=5, timeout=120, execute_kwargs=None):
    """Runs a notebook and displays the output in the master notebook.

    Executes a notebook, optionally passing "arguments" in a way roughly
    similar to passing arguments to a function.
    Notebook arguments are passed in a dictionary (`nb_kwargs`) which is
    converted to a string containing python code, then inserted in the notebook
    as a code cell. The code contains only assignments of variables which
    can be used to control the execution of a suitably written notebook. When
    calling a notebook, you need to know which arguments (variables) to pass.
    Differently from functions, no check on the input arguments is performed.

    Arguments:
        notebook_name (string): name of the notebook to be executed.
        nb_kwargs (dict or None): If not None, this dict is converted to a
            string of python assignments with keys representing variables
            names and values variables content. This string is inserted as
            code-cell in the notebook to be executed.
        insert_pos (int): position of insertion of the code-cell containing
            the input arguments. Default is 5 (i.e. sixth cell). With this
            default, the input notebook can define, in the first cell, default
            values of input arguments (used when the notebook is executed
            with no arguments or through the Notebook GUI).
        timeout (int): timeout in seconds after which the execution is aborted.
        execute_kwargs (dict): additional arguments passed to
            `ExecutePreprocessor`.
    """
    if nb_kwargs is not None:
        header = '# Cell inserted during automated execution.'
        code = dict_to_code(nb_kwargs)
        code_cell = '\n'.join((header, code))

    if execute_kwargs is None:
        execute_kwargs = {}
    ep = ExecutePreprocessor(timeout=timeout, **execute_kwargs)
    nb = nbformat.read(notebook_name, as_version=4)
    if len(nb_kwargs) > 0:
        nb['cells'].insert(insert_pos, nbformat.v4.new_code_cell(code_cell))

    try:
        # Execute the notebook
        ep.preprocess(nb, {'metadata': {'path': './'}})
#*****************************************
#    Title: analysis.ipynb
#    Author: Benjamin RK
#    Date: April 2013
#    Availability: https://gist.github.com/minrk/5491090

        ip = get_ipython()
        for cell in nb.cells:
            if cell.cell_type != 'code':
                continue
            ip.run_cell(cell.source)
#*****************************************
    except:
        # Execution failed, print a message then raise.
        msg = 'Error executing the notebook "%s".\n\n' % notebook_name
        print(msg)
        raise

def nb_to_html(root, template='basic', version=4, timeout=600, kernel='python3'):
    '''
    This functions executes a Jupyter notebook and creates the related
    HTML file.

    Args:
        root (str): name of the file without the .ipynb extension
        template (str): name of the template (to be in the current folder as template.tpl)
        version (int): version of the notebook
        timeout (float): maximum time spent per cell
        kernel (str)

    Returns:
        None

    The function executes root.ipynb into root_exe.ipynb and creates the file root.html.
    '''
    with open(root + '.ipynb') as f:
        nb = nbformat.read(f, as_version=version)

    ep = ExecutePreprocessor(timeout=timeout, kernel_name=kernel)
    ep.preprocess(nb, {'metadata': {'path': '.'}})

    with open(root + '_exe.ipynb', 'wt') as f:
        nbformat.write(nb, f)

    html_exporter = HTMLExporter()
    html_exporter.template_file = template

    with open(root + '_exe.ipynb', mode='r') as f:
        notebook = nbformat.reads(''.join(f.readlines()), as_version=version)
        (body, _) = html_exporter.from_notebook_node(notebook)
        codecs.open(root + '.html', 'w', encoding='utf-8').write(body)

    def execute(self):
        print("Cleaning lowfat/reports/html ...")
        old_reports = os.listdir("lowfat/reports/html")
        for old_report in old_reports:
            print("- Removing lowfat/reports/html/{}".format(old_report))
            os.remove("lowfat/reports/html/{}".format(old_report))
        print("Cleaning of lowfat/reports/html is complete.")

        notebook_filenames = os.listdir("lowfat/reports")

        for notebook_filename in notebook_filenames:
            if not notebook_filename.endswith(".ipynb"):
                continue

            print("Processing lowfat/reports/{}".format(notebook_filename))

            # Based on Executing notebooks, nbconvert Documentation by Jupyter Development Team.
            # https://nbconvert.readthedocs.io/en/latest/execute_api.html
            with open("lowfat/reports/{}".format(notebook_filename)) as file_:
                notebook = nbformat.read(file_, as_version=4)

                # Kernel is provided by https://github.com/django-extensions/django-extensions/
                execute_preprocessor = ExecutePreprocessor(timeout=600, kernel_name='django_extensions')
                execute_preprocessor.preprocess(notebook, {'metadata': {'path': '.'}})

                html_exporter = HTMLExporter()
                html_exporter.template_file = 'basic'

                (body, dummy_resources) = html_exporter.from_notebook_node(notebook)

                with open('lowfat/reports/html/{}.html'.format(notebook_filename), 'wt') as file_:
                    file_.write(body)

def execute_nb(src, dst, allow_errors=False, timeout=1000, kernel_name=None):
    """
    Execute notebook in `src` and write the output to `dst`

    Parameters
    ----------
    src, dst: str
        path to notebook
    allow_errors: bool
    timeout: int
    kernel_name: str
        defualts to value set in notebook metadata

    Returns
    -------
    dst: str
    """
    with io.open(src, encoding="utf-8") as f:
        nb = nbformat.read(f, as_version=4)

    ep = ExecutePreprocessor(allow_errors=allow_errors, timeout=timeout, kernel_name=kernel_name)
    ep.preprocess(nb, {"metadta": {"path": "notebooks/"}})

    with io.open(dst, "wt", encoding="utf-8") as f:
        nbformat.write(nb, f)
    return dst

def _notebook_run(path):
    """Execute a notebook via nbconvert and collect output.
       :returns (parsed nb object, execution errors)
    """
    kernel_name = "python%d" % sys.version_info[0]
    this_file_directory = os.path.dirname(__file__)
    errors = []
    with tempfile.NamedTemporaryFile(suffix=".ipynb", mode="wt") as fout:
        with open(path) as f:
            nb = nbformat.read(f, as_version=4)
            nb.metadata.get("kernelspec", {})["name"] = kernel_name
            ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=10)

            try:
                ep.preprocess(nb, {"metadata": {"path": this_file_directory}})
            except CellExecutionError as e:
                if "SKIP" in e.traceback:
                    print(str(e.traceback).split("\n")[-2])
                else:
                    raise e
            except TimeoutError as e:
                print(e)

            finally:
                nbformat.write(nb, fout)
        # nb = nbformat.read(fout, nbformat.current_nbformat)

    # errors = errors.extend(
    # [output for cell in nb.cells if "outputs" in cell
    # for output in cell["outputs"] if output.output_type == "error"])

    return nb, errors

def test_notebook(notebook):
    nb_name = os.path.split(notebook)[-1]
    if nb_name in SLOW_NOTEBOOKS:
        pytest.skip('Notebook is too slow to test')
    nb = nbformat.read(notebook, as_version=4)
    ep = ExecutePreprocessor(allow_errors=False,
                             timeout=240,
                             kernel_name=kernel_name)
    ep.preprocess(nb, {'metadata': {'path': NOTEBOOK_DIR}})

def run_ipynb(fs):
    """
    """
    with open(fs) as f:
        nb = nbformat.read(f, as_version=4)
    ep = ExecutePreprocessor()
    
    ep.preprocess(nb, {'metadata': {'path': os.path.dirname(fs)}})
    with open(fs, 'wt') as f:
        nbformat.write(nb, fs)

def write_notebook(cells, outputfile, execute=True, kernel='python3'):
    kernelspec = get_kernelspec(kernel)
    notebook = new_notebook(cells=cells,
                            metadata={'language': 'python',
                                      'kernelspec': kernelspec})

    if execute:
        ep = ExecutePreprocessor(timeout=600, kernelname='python3')
        ep.preprocess(notebook,
                      {'metadata': {'path': os.path.dirname(outputfile)}})

    nbformat.write(notebook, outputfile)

def _test_tutorial_nb(tutorial):
    """Run tutorial jupyter notebook to catch any execution error.

    Parameters
    ----------
    tutorial : str
        tutorial name in folder/tutorial format
    """

    tutorial_dir = os.path.join(os.path.dirname(__file__), '..', '..', 'docs', '_build', 'html', 'tutorials')
    tutorial_path = os.path.join(*([tutorial_dir] + tutorial.split('/')))

    # see env variable docs in the doc string of the file
    kernel = os.getenv('MXNET_TUTORIAL_TEST_KERNEL', None)
    no_cache = os.getenv('MXNET_TUTORIAL_TEST_NO_CACHE', False)

    working_dir = os.path.join(*([temp_dir] + tutorial.split('/')))

    if no_cache == '1':
        print("Cleaning and setting up temp directory '{}'".format(working_dir))
        shutil.rmtree(temp_dir, ignore_errors=True)

    errors = []
    notebook = None
    if not os.path.isdir(working_dir):
        os.makedirs(working_dir)
    try:
        notebook = nbformat.read(tutorial_path + '.ipynb', as_version=IPYTHON_VERSION)
        # Adding a small delay to allow time for sockets to be freed
        # stop-gap measure to battle the 1000ms linger of socket hard coded
        # in the kernel API code
        time.sleep(1.1) 
        if kernel is not None:
            eprocessor = ExecutePreprocessor(timeout=TIME_OUT, kernel_name=kernel)
        else:
            eprocessor = ExecutePreprocessor(timeout=TIME_OUT)
        nb, _ = eprocessor.preprocess(notebook, {'metadata': {'path': working_dir}})
    except Exception as err:
        err_msg = str(err)
        errors.append(err_msg)
    finally:
        if notebook is not None:
            output_file = os.path.join(working_dir, "output.txt")
            nbformat.write(notebook, output_file)
            output_nb = open(output_file, mode='r')
            for line in output_nb:
                if "Warning:" in line:
                    errors.append("Warning:\n"+line)
        if len(errors) > 0:
            print('\n'.join(errors))
            return False
        return True