#!/usr/bin/env python3
#
# Copyright (c) <NAME> and the University of Texas MD Anderson Cancer Center
# Distributed under the terms of the 3-clause BSD License.

import argparse
import re
import sys
import time
from io import StringIO

import nbformat
from nbconvert.exporters import Exporter
from nbconvert.preprocessors.execute import ExecutePreprocessor, CellExecutionError
from nbformat.v4 import new_code_cell, new_markdown_cell, new_notebook, output_from_msg

from sos.converter import extract_workflow
from sos.syntax import SOS_SECTION_HEADER
from sos.utils import env

#
# Converter from Notebook
#


def get_notebook_to_script_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.sos (or --to sos)',
                                     description='''Export Jupyter notebook with a SoS kernel to a
        .sos file. The cells are presented in the .sos file as
        cell structure lines, which will be ignored if executed
        in batch mode ''')
    return parser


# This class cannot be defined in .kernel because it would cause some
# weird problem with unittesting not able to resolve __main__
class SoS_Exporter(Exporter):
    def __init__(self, config=None, **kwargs):
        self.output_extension = '.sos'
        self.output_mimetype = 'text/x-sos'
        Exporter.__init__(self, config, **kwargs)

    def from_notebook_cell(self, cell, fh, idx=0):
        # in non-all mode, markdown cells are ignored because they can be mistakenly
        # treated as markdown content of an action or script #806
        if cell.cell_type != "code":
            return
        #
        # Non-sos code cells are also ignored
        if 'kernel' in cell.metadata and cell.metadata['kernel'] not in ('sos', 'SoS', None):
            return
        lines = cell.source.split('\n')
        valid_cell = False
        for idx, line in enumerate(lines):
            if valid_cell or (line.startswith('%include') or line.startswith('%from')):
                fh.write(line + '\n')
            elif SOS_SECTION_HEADER.match(line):
                valid_cell = True
                # look retrospectively for comments
                c = idx - 1
                comment = ''
                while c >= 0 and lines[c].startswith('#'):
                    comment = lines[c] + '\n' + comment
                    c -= 1
                fh.write(comment + line + '\n')
            # other content, namely non-%include lines before section header is ignored
        if valid_cell:
            fh.write('\n')
        return idx

    def from_notebook_node(self, nb, resources, **kwargs):
        #
        cells = nb.cells
        with StringIO() as fh:
            fh.write('#!/usr/bin/env sos-runner\n')
            fh.write('#fileformat=SOS1.0\n\n')
            idx = 0
            for cell in cells:
                idx = self.from_notebook_cell(cell, fh, idx)
            content = fh.getvalue()
        resources['output_extension'] = '.sos'
        return content, resources


def notebook_to_script(notebook_file, sos_file, args=None, unknown_args=None):
    '''
    Convert a ipython notebook to sos format.
    '''
    if unknown_args:
        raise ValueError(f'Unrecognized parameter {unknown_args}')
    exporter = SoS_Exporter()
    notebook = nbformat.read(notebook_file, nbformat.NO_CONVERT)
    output, _ = exporter.from_notebook_node(notebook, {})
    if not sos_file:
        sys.stdout.write(output)
    elif isinstance(sos_file, str):
        with open(sos_file, 'w') as sos:
            sos.write(output)
        env.logger.info(f'SoS script saved to {sos_file}')
    else:
        sos_file.write(output)

#
# Converter to Notebook
#


def get_script_to_notebook_parser():
    parser = argparse.ArgumentParser('sos convert FILE.sos FILE._ipynb (or --to ipynb)',
                                     description='''Convert a sos script to Jupyter notebook (.ipynb)
            so that it can be opened by Jupyter notebook.''')
    return parser


def add_cell(cells, content, cell_type, cell_count, metainfo):
    # if a section consist of all report, report it as a markdown cell
    if not content:
        return
    if cell_type not in ('code', 'markdown'):
        env.logger.warning(
            f'Unrecognized cell type {cell_type}, code assumed.')
    if cell_type == 'markdown' and any(x.strip() and not x.startswith('#! ') for x in content):
        env.logger.warning(
            'Markdown lines not starting with #!, code cell assumed.')
        cell_type = 'code'
    #
    if cell_type == 'markdown':
        cells.append(new_markdown_cell(source=''.join([x[3:] for x in content]).strip(),
                                       metadata=metainfo))
    else:
        cells.append(
            new_code_cell(
                # remove any trailing blank lines...
                source=''.join(content).strip(),
                execution_count=cell_count,
                metadata=metainfo)
        )


class SoS_ExecutePreprocessor(ExecutePreprocessor):
    def __init__(self, filename, *args, **kwargs):
        super(SoS_ExecutePreprocessor, self).__init__(*args, **kwargs)
        self._filename = filename

    def _prepare_meta(self, cell):
        meta = {}
        run_notebook = re.search(
            r'^%sosrun($|\s)|^%sossave($|\s)|^%preview\s.*(-w|--workflow).*$', cell.source, re.MULTILINE)
        if run_notebook:
            meta['workflow'] = self._workflow
        if re.search(r'^%toc\s/', cell.source, re.MULTILINE):
            meta['toc'] = self._toc
        meta['path'] = self._filename
        meta['use_panel'] = False
        meta['rerun'] = False
        # ID is dynamically generated by the frontend and does not exist
        # in the backend for batch mode
        meta['cell_id'] = 0
        meta['batch_mode'] = True
        meta['cell_kernel'] = cell.metadata.kernel
        return meta

    def run_cell(self, cell, cell_index=0):
        # sos is the additional meta information sent to kernel
        content = dict(code=cell.source, silent=False, store_history=False,
                       user_expressions='',
                       allow_stdin=False, stop_on_error=False,
                       sos=self._prepare_meta(cell))
        msg = self.kc.session.msg('execute_request', content)
        self.kc.shell_channel.send(msg)
        msg_id = msg['header']['msg_id']

        # the reset is copied from https://github.com/jupyter/nbconvert/blob/master/nbconvert/preprocessors/execute.py
        # because we only need to change the first line

        #  msg_id = self.kc.execute(cell.source)

        self.log.debug("Executing cell:\n%s", cell.source)
        exec_reply = self._wait_for_reply(msg_id, cell)

        outs = cell.outputs = []

        while True:
            try:
                # We've already waited for execute_reply, so all output
                # should already be waiting. However, on slow networks, like
                # in certain CI systems, waiting < 1 second might miss messages.
                # So long as the kernel sends a status:idle message when it
                # finishes, we won't actually have to wait this long, anyway.
                msg = self.kc.iopub_channel.get_msg(timeout=self.iopub_timeout)
            except Empty:
                self.log.warning("Timeout waiting for IOPub output")
                if self.raise_on_iopub_timeout:
                    raise RuntimeError("Timeout waiting for IOPub output")
                else:
                    break
            if msg['parent_header'].get('msg_id') != msg_id:
                # not an output from our execution
                continue

            msg_type = msg['msg_type']
            self.log.debug("output: %s", msg_type)
            content = msg['content']

            # set the prompt number for the input and the output
            if 'execution_count' in content:
                cell['execution_count'] = content['execution_count']

            if msg_type == 'status':
                if content['execution_state'] == 'idle':
                    break
                else:
                    continue
            elif msg_type == 'execute_input':
                continue
            elif msg_type == 'clear_output':
                outs[:] = []
               # clear display_id mapping for this cell
                for display_id, cell_map in self._display_id_map.items():
                    if cell_index in cell_map:
                        cell_map[cell_index] = []
                continue
            elif msg_type.startswith('comm'):
                continue

            display_id = None
            if msg_type in {'execute_result', 'display_data', 'update_display_data'}:
                display_id = msg['content'].get(
                    'transient', {}).get('display_id', None)
                if display_id:
                    self._update_display_id(display_id, msg)
                if msg_type == 'update_display_data':
                    # update_display_data doesn't get recorded
                    continue

            try:
                out = output_from_msg(msg)
            except ValueError:
                self.log.error("unhandled iopub msg: " + msg_type)
                continue
            if display_id:
                # record output index in:
                #   _display_id_map[display_id][cell_idx]
                cell_map = self._display_id_map.setdefault(display_id, {})
                output_idx_list = cell_map.setdefault(cell_index, [])
                output_idx_list.append(len(outs))

            outs.append(out)

        return exec_reply, outs

    def _scan_table_of_content(self, nb):
        cells = nb.cells
        TOC = ''
        for cell in cells:
            if cell.cell_type == "markdown":
                for line in cell.source.splitlines():
                    if re.match('^#+ ', line):
                        TOC += line + '\n'
        return TOC

    def preprocess(self, nb, *args, **kwargs):
        self._workflow = extract_workflow(nb)
        self._toc = self._scan_table_of_content(nb)
        return super(SoS_ExecutePreprocessor, self).preprocess(nb, *args, **kwargs)


def script_to_notebook(script_file, notebook_file, args=None, unknown_args=None):
    '''
    Convert a sos script to iPython notebook (.ipynb) so that it can be opened
    by Jupyter notebook.
    '''
    if unknown_args:
        raise ValueError(f'Unrecognized parameter {unknown_args}')
    cells = []
    cell_count = 1
    cell_type = 'code'
    metainfo = {}
    content = []

    with open(script_file) as script:
        first_block = True
        for line in script:
            if line.startswith('#') and first_block:
                if line.startswith('#!'):
                    continue
                if line.startswith('#fileformat='):
                    if not line[12:].startswith('SOS'):
                        raise RuntimeError(
                            f'{script_file} is not a SoS script according to #fileformat line.')
                    continue

            first_block = False

            mo = SOS_SECTION_HEADER.match(line)
            if mo:
                # get ride of empty content
                if not any(x.strip() for x in content):
                    content = []

                if content:
                    add_cell(cells, content, cell_type, cell_count, metainfo)

                cell_type = 'code'
                cell_count += 1
                metainfo = {'kernel': 'SoS'}
                content = [line]
                continue

            if line.startswith('#!'):
                if cell_type == 'markdown':
                    content.append(line)
                    continue
                else:
                    # get ride of empty content
                    if not any(x.strip() for x in content):
                        content = []

                    if content:
                        add_cell(cells, content, cell_type,
                                 cell_count, metainfo)

                    cell_type = 'markdown'
                    cell_count += 1
                    content = [line]
                    continue

            # other cases
            content.append(line)
    #
    if content and any(x.strip() for x in content):
        add_cell(cells, content, cell_type, cell_count, metainfo)
    #
    nb = new_notebook(cells=cells,
                      metadata={
                          'kernelspec': {
                              "display_name": "SoS",
                              "language": "sos",
                              "name": "sos"
                          },
                          "language_info": {
                              'codemirror_mode': 'sos',
                              "file_extension": ".sos",
                              "mimetype": "text/x-sos",
                              "name": "sos",
                              "pygments_lexer": "python",
                              'nbconvert_exporter': 'sos_notebook.converter.SoS_Exporter',
                          },
                          'sos': {
                              'kernels': [
                                  ['SoS', 'sos', '', '']
                              ]
                          }
                      }
                      )
    if not notebook_file:
        nbformat.write(nb, sys.stdout, 4)
    else:
        with open(notebook_file, 'w') as notebook:
            nbformat.write(nb, notebook, 4)
        env.logger.info(f'Jupyter notebook saved to {notebook_file}')
    # if err:
    #    raise RuntimeError(repr(err))


#
# notebook to HTML
#

def export_notebook(exporter_class, to_format, notebook_file, output_file, unknown_args=None, view=False):

    import os
    import subprocess
    if not os.path.isfile(notebook_file):
        raise RuntimeError(f'{notebook_file} does not exist')
    cfg_file = os.path.join(os.path.expanduser('~'), '.sos', 'nbconfig.py')
    if not os.path.isfile(cfg_file):
        with open(cfg_file, 'w') as cfg:
            cfg.write(f'''
import os
import sos
import sos_notebook

c = get_config()
c.TemplateExporter.template_path.extend([
  os.path.join(os.path.split(os.path.abspath(sos.__file__))[0], 'templates'),
  os.path.join(os.path.split(os.path.abspath(sos_notebook.__file__))[0], 'templates')])
''')
    if not output_file:
        import tempfile
        tmp = tempfile.NamedTemporaryFile(
            delete=False, suffix='.' + to_format).name
        tmp_stderr = tempfile.NamedTemporaryFile(
            delete=False, suffix='.' + to_format).name
        with open(tmp_stderr, 'w') as err:
            ret = subprocess.call(['jupyter', 'nbconvert', notebook_file, '--to', to_format,
                                   '--output', tmp, '--config', cfg_file] + ([] if unknown_args is None else unknown_args), stderr=err)
        with open(tmp_stderr) as err:
            err_msg = err.read()
        if ret != 0:
            env.logger.error(err_msg)
            env.logger.error(
                f'Failed to convert {notebook_file} to {to_format} format')
        else:
            # identify output files
            dest_file = err_msg.rsplit()[-1]
            if not os.path.isfile(dest_file):
                env.logger.error(err_msg)
                env.logger.error('Failed to get converted file.')
            elif view:
                import webbrowser
                url = f'file://{os.path.abspath(dest_file)}'
                env.logger.info(f'Viewing {url} in a browser')
                webbrowser.open(url, new=2)
                # allow browser some time to process the file before this process removes it
                time.sleep(2)
            else:
                with open(dest_file, 'rb') as tfile:
                    sys.stdout.buffer.write(tfile.read())
        try:
            os.remove(tmp)
        except Exception:
            pass
    else:
        ret = subprocess.call(['jupyter', 'nbconvert', os.path.abspath(notebook_file), '--to', to_format,
                               '--output', os.path.abspath(output_file), '--config', cfg_file] + ([] if unknown_args is None else unknown_args))
        if ret != 0:
            env.logger.error(
                f'Failed to convert {notebook_file} to {to_format} format')
        else:
            env.logger.info(f'Output saved to {output_file}')


def get_notebook_to_html_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.html (or --to html)',
                                     description='''Export Jupyter notebook with a SoS kernel to a
        .html file. Additional command line arguments are passed directly to
        command "jupyter nbconvert --to html" so please refer to nbconvert manual for
        available options.''')
    parser.add_argument('--template',
                        help='''Template to export Jupyter notebook with sos kernel. SoS provides a number
        of templates, with sos-report displays markdown cells and only output of cells with
        prominent tag, and a control panel to control the display of the rest of the content
        ''')
    parser.add_argument('-e', '--execute', action='store_true',
                        help='''Execute the notebook in batch mode (as if running "Cell -> Run All"
                          from Jupyter notebook interface before converting to HTML''')
    parser.add_argument('-v', '--view', action='store_true',
                        help='''Open the output file in a broswer. In case no html file is specified,
        this option will display the HTML file in a browser, instead of writing its
        content to standard output.''')
    return parser


def notebook_to_html(notebook_file, output_file, sargs=None, unknown_args=None):
    from nbconvert.exporters.html import HTMLExporter
    import os
    if unknown_args is None:
        unknown_args = []
    if sargs and sargs.execute:
        # the step can take long time to complete
        ep = SoS_ExecutePreprocessor(notebook_file, timeout=60000)
        try:
            nb = nbformat.read(notebook_file, nbformat.NO_CONVERT)
            ep.preprocess(nb, {'metadata': {'path': '.'}})
            import tempfile
            tmp_file = os.path.join(env.temp_dir, os.path.basename(notebook_file))
            with open(tmp_file, 'w') as tmp_nb:
                nbformat.write(nb, tmp_nb, 4)
            notebook_file = tmp_file
        except CellExecutionError as e:
            env.logger.error(f'Failed to execute notebook: {e}')
    if sargs.template:
        unknown_args = ['--template', os.path.abspath(sargs.template) if os.path.isfile(
            sargs.template) else sargs.template] + unknown_args
    export_notebook(HTMLExporter, 'html', notebook_file,
                    output_file, unknown_args, view=sargs.view)


def get_notebook_to_pdf_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.pdf (or --to pdf)',
                                     description='''Export Jupyter notebook with a SoS kernel to a
        .pdf file. Additional command line arguments are passed directly to
        command "jupyter nbconvert --to pdf" so please refer to nbconvert manual for
        available options.''')
    parser.add_argument('--template',
                        help='''Template to export Jupyter notebook with sos kernel. SoS provides a number
        of templates, with sos-report displays markdown cells and only output of cells with
        prominent tag, and a control panel to control the display of the rest of the content
        ''')
    return parser


def notebook_to_pdf(notebook_file, output_file, sargs=None, unknown_args=None):
    from nbconvert.exporters.pdf import PDFExporter
    import os
    if unknown_args is None:
        unknown_args = []
    if sargs.template:
        unknown_args = ['--template', os.path.abspath(sargs.template) if os.path.isfile(
            sargs.template) else sargs.template] + unknown_args
    # jupyter convert will add extension to output file...
    if output_file is not None and output_file.endswith('.pdf'):
        output_file = output_file[:-4]
    export_notebook(PDFExporter, 'pdf', notebook_file,
                    output_file, unknown_args)


def get_notebook_to_md_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.md (or --to md)',
                                     description='''Export Jupyter notebook with a SoS kernel to a
        markdown file. Additional command line arguments are passed directly to
        command "jupyter nbconvert --to markdown" so please refer to nbconvert manual for
        available options.''')
    return parser


def notebook_to_md(notebook_file, output_file, sargs=None, unknown_args=None):
    from nbconvert.exporters.markdown import MarkdownExporter
    export_notebook(MarkdownExporter, 'markdown',
                    notebook_file, output_file, unknown_args)


def get_notebook_to_notebook_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.ipynb (or --to ipynb)',
                                     description='''Export a Jupyter notebook with a non-SoS kernel to a
        SoS notebook with SoS kernel. A SoS notebook will simply be copied to
        the destination file.''')
    parser.add_argument('--python3-to-sos', action='store_true',
                        help='''Convert python3 cells to SoS.''')
    parser.add_argument('--inplace', action='store_true',
                        help='''Overwrite input notebook with the output.''')
    return parser


def notebook_to_notebook(notebook_file, output_file, sargs=None, unknown_args=None):
    notebook = nbformat.read(notebook_file, nbformat.NO_CONVERT)
    # get the kernel of the notebook
    # this is like 'R', there is another 'display_name'
    lan_name = notebook['metadata']['kernelspec']['language']
    # this is like 'ir'
    kernel_name = notebook['metadata']['kernelspec']['name']
    if kernel_name == 'sos':
        # already a SoS notebook?
        if sargs.inplace:
            return
        if output_file:
            import shutil
            shutil.copy(notebook_file, output_file)
        else:
            with open(notebook_file) as nb:
                sys.stdout.write(nb.read())
        return
    # convert to?
    elif kernel_name == 'python3' and sargs.python3_to_sos:
        to_lan = 'SoS'
        to_kernel = 'sos'
    else:
        to_lan = lan_name
        to_kernel = kernel_name
    # write all cells
    #
    cells = []
    for cell in notebook.cells:
        if cell.cell_type == 'code':
            cell.metadata['kernel'] = to_lan
        cells.append(cell)
    #
    # create header
    nb = new_notebook(cells=cells,
                      metadata={
                          'kernelspec': {
                              "display_name": "SoS",
                              "language": "sos",
                              "name": "sos"
                          },
                          "language_info": {
                              "file_extension": ".sos",
                              "mimetype": "text/x-sos",
                              "name": "sos",
                              "pygments_lexer": "python",
                              'nbconvert_exporter': 'sos_notebook.converter.SoS_Exporter',
                          },
                          'sos': {
                              'kernels': [
                                  ['SoS', 'sos', '', '']] +
                              ([[to_lan, to_kernel, '', '']]
                               if to_lan != 'SoS' else []),
                              'default_kernel': to_lan
                          }
                      }
                      )

    if sargs.inplace:
        with open(notebook_file, 'w') as new_nb:
            nbformat.write(nb, new_nb, 4)
        env.logger.info(f'Jupyter notebook saved to {notebook_file}')
    elif not output_file:
        nbformat.write(nb, sys.stdout, 4)
    else:
        with open(output_file, 'w') as new_nb:
            nbformat.write(nb, new_nb, 4)
        env.logger.info(f'Jupyter notebook saved to {output_file}')


def get_Rmarkdown_to_notebook_parser():
    parser = argparse.ArgumentParser('sos convert FILE.Rmd FILE.ipynb (or --to ipynb)',
                                     description='''Export a Rmarkdown file kernel to a SoS notebook. It currently
        only handles code block and Markdown, and not inline expression.''')
    return parser


def Rmarkdown_to_notebook(rmarkdown_file, output_file, sargs=None, unknown_args=None):
    #
    with open(rmarkdown_file) as script:
        content = script.read()
    #
    # identify the headers
    header = header = re.compile('^(#+\s.*$)', re.M)
    paragraphs = re.split(header, content)
    #
    cells = []
    cell_count = 1
    for idx, p in enumerate(paragraphs):
        if idx % 2 == 1:
            # this is header, let us create a markdown cell
            cells.append(
                new_markdown_cell(
                    source=p.strip()))
        else:
            # this is unknown yet, let us find ```{} block
            code = re.compile('^\s*(```{.*})$', re.M)
            endcode = re.compile('^\s*```$', re.M)

            for pidx, pc in enumerate(re.split(code, p)):
                if pidx == 0:
                    # piece before first code block. it might contain
                    # inline expression
                    cells.append(
                        new_markdown_cell(
                            source=pc.strip())
                    )
                elif pidx % 2 == 0:
                    # this is AFTER the {r} piece, let us assume all R code
                    # for now
                    # this is code, but it should end somewhere
                    pieces = re.split(endcode, pc)
                    # I belive that we should have
                    #   pieces[0] <- code
                    #   pieces[1] <- rest...
                    # but I could be wrong.
                    cells.append(
                        new_code_cell(
                            source=pieces[0],
                            execution_count=cell_count,
                            metadata={'kernel': 'R'}
                        )
                    )
                    cell_count += 1
                    #
                    for piece in pieces[1:]:
                        cells.append(
                            new_markdown_cell(
                                source=piece.strip())
                        )
    #
    # create header
    nb = new_notebook(cells=cells,
                      metadata={
                          'kernelspec': {
                              "display_name": "SoS",
                              "language": "sos",
                              "name": "sos"
                          },
                          "language_info": {
                              "file_extension": ".sos",
                              "mimetype": "text/x-sos",
                              "name": "sos",
                              "pygments_lexer": "python",
                              'nbconvert_exporter': 'sos_notebook.converter.SoS_Exporter',
                          },
                          'sos': {
                              'kernels': [
                                  ['SoS', 'sos', '', ''],
                                  ['R', 'ir', '', '']],
                              'default_kernel': 'R'
                          }
                      }
                      )

    if not output_file:
        nbformat.write(nb, sys.stdout, 4)
    else:
        with open(output_file, 'w') as new_nb:
            nbformat.write(nb, new_nb, 4)
        env.logger.info(f'Jupyter notebook saved to {output_file}')

#!/usr/bin/env python3
#
# Copyright (c) <NAME> and the University of Texas MD Anderson Cancer Center
# Distributed under the terms of the 3-clause BSD License.

import argparse
import re
import sys
import time
from io import StringIO

import nbformat
from nbconvert.exporters import Exporter
from nbconvert.preprocessors.execute import ExecutePreprocessor, CellExecutionError
from nbformat.v4 import new_code_cell, new_markdown_cell, new_notebook, output_from_msg

from sos.converter import extract_workflow
from sos.syntax import SOS_SECTION_HEADER
from sos.utils import env

#
# Converter from Notebook
#


def get_notebook_to_script_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.sos (or --to sos)',
                                     description='''Export Jupyter notebook with a SoS kernel to a
        .sos file. The cells are presented in the .sos file as
        cell structure lines, which will be ignored if executed
        in batch mode ''')
    return parser


# This class cannot be defined in .kernel because it would cause some
# weird problem with unittesting not able to resolve __main__
class SoS_Exporter(Exporter):
    def __init__(self, config=None, **kwargs):
        self.output_extension = '.sos'
        self.output_mimetype = 'text/x-sos'
        Exporter.__init__(self, config, **kwargs)

    def from_notebook_cell(self, cell, fh, idx=0):
        # in non-all mode, markdown cells are ignored because they can be mistakenly
        # treated as markdown content of an action or script #806
        if cell.cell_type != "code":
            return
        #
        # Non-sos code cells are also ignored
        if 'kernel' in cell.metadata and cell.metadata['kernel'] not in ('sos', 'SoS', None):
            return
        lines = cell.source.split('\n')
        valid_cell = False
        for idx, line in enumerate(lines):
            if valid_cell or (line.startswith('%include') or line.startswith('%from')):
                fh.write(line + '\n')
            elif SOS_SECTION_HEADER.match(line):
                valid_cell = True
                # look retrospectively for comments
                c = idx - 1
                comment = ''
                while c >= 0 and lines[c].startswith('#'):
                    comment = lines[c] + '\n' + comment
                    c -= 1
                fh.write(comment + line + '\n')
            # other content, namely non-%include lines before section header is ignored
        if valid_cell:
            fh.write('\n')
        return idx

    def from_notebook_node(self, nb, resources, **kwargs):
        #
        cells = nb.cells
        with StringIO() as fh:
            fh.write('#!/usr/bin/env sos-runner\n')
            fh.write('#fileformat=SOS1.0\n\n')
            idx = 0
            for cell in cells:
                idx = self.from_notebook_cell(cell, fh, idx)
            content = fh.getvalue()
        resources['output_extension'] = '.sos'
        return content, resources


def notebook_to_script(notebook_file, sos_file, args=None, unknown_args=None):
    '''
    Convert a ipython notebook to sos format.
    '''
    if unknown_args:
        raise ValueError(f'Unrecognized parameter {unknown_args}')
    exporter = SoS_Exporter()
    notebook = nbformat.read(notebook_file, nbformat.NO_CONVERT)
    output, _ = exporter.from_notebook_node(notebook, {})
    if not sos_file:
        sys.stdout.write(output)
    elif isinstance(sos_file, str):
        with open(sos_file, 'w') as sos:
            sos.write(output)
        env.logger.info(f'SoS script saved to {sos_file}')
    else:
        sos_file.write(output)

#
# Converter to Notebook
#


def get_script_to_notebook_parser():
    parser = argparse.ArgumentParser('sos convert FILE.sos FILE._ipynb (or --to ipynb)',
                                     description='''Convert a sos script to Jupyter notebook (.ipynb)
            so that it can be opened by Jupyter notebook.''')
    return parser


def add_cell(cells, content, cell_type, cell_count, metainfo):
    # if a section consist of all report, report it as a markdown cell
    if not content:
        return
    if cell_type not in ('code', 'markdown'):
        env.logger.warning(
            f'Unrecognized cell type {cell_type}, code assumed.')
    if cell_type == 'markdown' and any(x.strip() and not x.startswith('#! ') for x in content):
        env.logger.warning(
            'Markdown lines not starting with #!, code cell assumed.')
        cell_type = 'code'
    #
    if cell_type == 'markdown':
        cells.append(new_markdown_cell(source=''.join([x[3:] for x in content]).strip(),
                                       metadata=metainfo))
    else:
        cells.append(
            new_code_cell(
                # remove any trailing blank lines...
                source=''.join(content).strip(),
                execution_count=cell_count,
                metadata=metainfo)
        )


class SoS_ExecutePreprocessor(ExecutePreprocessor):
    def __init__(self, filename, *args, **kwargs):
        super(SoS_ExecutePreprocessor, self).__init__(*args, **kwargs)
        self._filename = filename

    def _prepare_meta(self, cell):
        meta = {}
        run_notebook = re.search(
            r'^%sosrun($|\s)|^%sossave($|\s)|^%preview\s.*(-w|--workflow).*$', cell.source, re.MULTILINE)
        if run_notebook:
            meta['workflow'] = self._workflow
        if re.search(r'^%toc\s/', cell.source, re.MULTILINE):
            meta['toc'] = self._toc
        meta['path'] = self._filename
        meta['use_panel'] = False
        meta['rerun'] = False
        # ID is dynamically generated by the frontend and does not exist
        # in the backend for batch mode
        meta['cell_id'] = 0
        meta['batch_mode'] = True
        meta['cell_kernel'] = cell.metadata.kernel
        return meta

    def run_cell(self, cell, cell_index=0):
        # sos is the additional meta information sent to kernel
        content = dict(code=cell.source, silent=False, store_history=False,
                       user_expressions='',
                       allow_stdin=False, stop_on_error=False,
                       sos=self._prepare_meta(cell))
        msg = self.kc.session.msg('execute_request', content)
        self.kc.shell_channel.send(msg)
        msg_id = msg['header']['msg_id']

        # the reset is copied from https://github.com/jupyter/nbconvert/blob/master/nbconvert/preprocessors/execute.py
        # because we only need to change the first line

        #  msg_id = self.kc.execute(cell.source)

        self.log.debug("Executing cell:\n%s", cell.source)
        exec_reply = self._wait_for_reply(msg_id, cell)

        outs = cell.outputs = []

        while True:
            try:
                # We've already waited for execute_reply, so all output
                # should already be waiting. However, on slow networks, like
                # in certain CI systems, waiting < 1 second might miss messages.
                # So long as the kernel sends a status:idle message when it
                # finishes, we won't actually have to wait this long, anyway.
                msg = self.kc.iopub_channel.get_msg(timeout=self.iopub_timeout)
            except Empty:
                self.log.warning("Timeout waiting for IOPub output")
                if self.raise_on_iopub_timeout:
                    raise RuntimeError("Timeout waiting for IOPub output")
                else:
                    break
            if msg['parent_header'].get('msg_id') != msg_id:
                # not an output from our execution
                continue

            msg_type = msg['msg_type']
            self.log.debug("output: %s", msg_type)
            content = msg['content']

            # set the prompt number for the input and the output
            if 'execution_count' in content:
                cell['execution_count'] = content['execution_count']

            if msg_type == 'status':
                if content['execution_state'] == 'idle':
                    break
                else:
                    continue
            elif msg_type == 'execute_input':
                continue
            elif msg_type == 'clear_output':
                outs[:] = []
               # clear display_id mapping for this cell
                for display_id, cell_map in self._display_id_map.items():
                    if cell_index in cell_map:
                        cell_map[cell_index] = []
                continue
            elif msg_type.startswith('comm'):
                continue

            display_id = None
            if msg_type in {'execute_result', 'display_data', 'update_display_data'}:
                display_id = msg['content'].get(
                    'transient', {}).get('display_id', None)
                if display_id:
                    self._update_display_id(display_id, msg)
                if msg_type == 'update_display_data':
                    # update_display_data doesn't get recorded
                    continue

            try:
                out = output_from_msg(msg)
            except ValueError:
                self.log.error("unhandled iopub msg: " + msg_type)
                continue
            if display_id:
                # record output index in:
                #   _display_id_map[display_id][cell_idx]
                cell_map = self._display_id_map.setdefault(display_id, {})
                output_idx_list = cell_map.setdefault(cell_index, [])
                output_idx_list.append(len(outs))

            outs.append(out)

        return exec_reply, outs

    def _scan_table_of_content(self, nb):
        cells = nb.cells
        TOC = ''
        for cell in cells:
            if cell.cell_type == "markdown":
                for line in cell.source.splitlines():
                    if re.match('^#+ ', line):
                        TOC += line + '\n'
        return TOC

    def preprocess(self, nb, *args, **kwargs):
        self._workflow = extract_workflow(nb)
        self._toc = self._scan_table_of_content(nb)
        return super(SoS_ExecutePreprocessor, self).preprocess(nb, *args, **kwargs)


def script_to_notebook(script_file, notebook_file, args=None, unknown_args=None):
    '''
    Convert a sos script to iPython notebook (.ipynb) so that it can be opened
    by Jupyter notebook.
    '''
    if unknown_args:
        raise ValueError(f'Unrecognized parameter {unknown_args}')
    cells = []
    cell_count = 1
    cell_type = 'code'
    metainfo = {}
    content = []

    with open(script_file) as script:
        first_block = True
        for line in script:
            if line.startswith('#') and first_block:
                if line.startswith('#!'):
                    continue
                if line.startswith('#fileformat='):
                    if not line[12:].startswith('SOS'):
                        raise RuntimeError(
                            f'{script_file} is not a SoS script according to #fileformat line.')
                    continue

            first_block = False

            mo = SOS_SECTION_HEADER.match(line)
            if mo:
                # get ride of empty content
                if not any(x.strip() for x in content):
                    content = []

                if content:
                    add_cell(cells, content, cell_type, cell_count, metainfo)

                cell_type = 'code'
                cell_count += 1
                metainfo = {'kernel': 'SoS'}
                content = [line]
                continue

            if line.startswith('#!'):
                if cell_type == 'markdown':
                    content.append(line)
                    continue
                else:
                    # get ride of empty content
                    if not any(x.strip() for x in content):
                        content = []

                    if content:
                        add_cell(cells, content, cell_type,
                                 cell_count, metainfo)

                    cell_type = 'markdown'
                    cell_count += 1
                    content = [line]
                    continue

            # other cases
            content.append(line)
    #
    if content and any(x.strip() for x in content):
        add_cell(cells, content, cell_type, cell_count, metainfo)
    #
    nb = new_notebook(cells=cells,
                      metadata={
                          'kernelspec': {
                              "display_name": "SoS",
                              "language": "sos",
                              "name": "sos"
                          },
                          "language_info": {
                              'codemirror_mode': 'sos',
                              "file_extension": ".sos",
                              "mimetype": "text/x-sos",
                              "name": "sos",
                              "pygments_lexer": "python",
                              'nbconvert_exporter': 'sos_notebook.converter.SoS_Exporter',
                          },
                          'sos': {
                              'kernels': [
                                  ['SoS', 'sos', '', '']
                              ]
                          }
                      }
                      )
    if not notebook_file:
        nbformat.write(nb, sys.stdout, 4)
    else:
        with open(notebook_file, 'w') as notebook:
            nbformat.write(nb, notebook, 4)
        env.logger.info(f'Jupyter notebook saved to {notebook_file}')
    # if err:
    #    raise RuntimeError(repr(err))


#
# notebook to HTML
#

def export_notebook(exporter_class, to_format, notebook_file, output_file, unknown_args=None, view=False):

    import os
    import subprocess
    if not os.path.isfile(notebook_file):
        raise RuntimeError(f'{notebook_file} does not exist')
    cfg_file = os.path.join(os.path.expanduser('~'), '.sos', 'nbconfig.py')
    if not os.path.isfile(cfg_file):
        with open(cfg_file, 'w') as cfg:
            cfg.write(f'''
import os
import sos
import sos_notebook

c = get_config()
c.TemplateExporter.template_path.extend([
  os.path.join(os.path.split(os.path.abspath(sos.__file__))[0], 'templates'),
  os.path.join(os.path.split(os.path.abspath(sos_notebook.__file__))[0], 'templates')])
''')
    if not output_file:
        import tempfile
        tmp = tempfile.NamedTemporaryFile(
            delete=False, suffix='.' + to_format).name
        tmp_stderr = tempfile.NamedTemporaryFile(
            delete=False, suffix='.' + to_format).name
        with open(tmp_stderr, 'w') as err:
            ret = subprocess.call(['jupyter', 'nbconvert', notebook_file, '--to', to_format,
                                   '--output', tmp, '--config', cfg_file] + ([] if unknown_args is None else unknown_args), stderr=err)
        with open(tmp_stderr) as err:
            err_msg = err.read()
        if ret != 0:
            env.logger.error(err_msg)
            env.logger.error(
                f'Failed to convert {notebook_file} to {to_format} format')
        else:
            # identify output files
            dest_file = err_msg.rsplit()[-1]
            if not os.path.isfile(dest_file):
                env.logger.error(err_msg)
                env.logger.error('Failed to get converted file.')
            elif view:
                import webbrowser
                url = f'file://{os.path.abspath(dest_file)}'
                env.logger.info(f'Viewing {url} in a browser')
                webbrowser.open(url, new=2)
                # allow browser some time to process the file before this process removes it
                time.sleep(2)
            else:
                with open(dest_file, 'rb') as tfile:
                    sys.stdout.buffer.write(tfile.read())
        try:
            os.remove(tmp)
        except Exception:
            pass
    else:
        ret = subprocess.call(['jupyter', 'nbconvert', os.path.abspath(notebook_file), '--to', to_format,
                               '--output', os.path.abspath(output_file), '--config', cfg_file] + ([] if unknown_args is None else unknown_args))
        if ret != 0:
            env.logger.error(
                f'Failed to convert {notebook_file} to {to_format} format')
        else:
            env.logger.info(f'Output saved to {output_file}')


def get_notebook_to_html_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.html (or --to html)',
                                     description='''Export Jupyter notebook with a SoS kernel to a
        .html file. Additional command line arguments are passed directly to
        command "jupyter nbconvert --to html" so please refer to nbconvert manual for
        available options.''')
    parser.add_argument('--template',
                        help='''Template to export Jupyter notebook with sos kernel. SoS provides a number
        of templates, with sos-report displays markdown cells and only output of cells with
        prominent tag, and a control panel to control the display of the rest of the content
        ''')
    parser.add_argument('-e', '--execute', action='store_true',
                        help='''Execute the notebook in batch mode (as if running "Cell -> Run All"
                          from Jupyter notebook interface before converting to HTML''')
    parser.add_argument('-v', '--view', action='store_true',
                        help='''Open the output file in a broswer. In case no html file is specified,
        this option will display the HTML file in a browser, instead of writing its
        content to standard output.''')
    return parser


def notebook_to_html(notebook_file, output_file, sargs=None, unknown_args=None):
    from nbconvert.exporters.html import HTMLExporter
    import os
    if unknown_args is None:
        unknown_args = []
    if sargs and sargs.execute:
        # the step can take long time to complete
        ep = SoS_ExecutePreprocessor(notebook_file, timeout=60000)
        try:
            nb = nbformat.read(notebook_file, nbformat.NO_CONVERT)
            ep.preprocess(nb, {'metadata': {'path': '.'}})
            import tempfile
            tmp_file = os.path.join(env.temp_dir, os.path.basename(notebook_file))
            with open(tmp_file, 'w') as tmp_nb:
                nbformat.write(nb, tmp_nb, 4)
            notebook_file = tmp_file
        except CellExecutionError as e:
            env.logger.error(f'Failed to execute notebook: {e}')
    if sargs.template:
        unknown_args = ['--template', os.path.abspath(sargs.template) if os.path.isfile(
            sargs.template) else sargs.template] + unknown_args
    export_notebook(HTMLExporter, 'html', notebook_file,
                    output_file, unknown_args, view=sargs.view)


def get_notebook_to_pdf_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.pdf (or --to pdf)',
                                     description='''Export Jupyter notebook with a SoS kernel to a
        .pdf file. Additional command line arguments are passed directly to
        command "jupyter nbconvert --to pdf" so please refer to nbconvert manual for
        available options.''')
    parser.add_argument('--template',
                        help='''Template to export Jupyter notebook with sos kernel. SoS provides a number
        of templates, with sos-report displays markdown cells and only output of cells with
        prominent tag, and a control panel to control the display of the rest of the content
        ''')
    return parser


def notebook_to_pdf(notebook_file, output_file, sargs=None, unknown_args=None):
    from nbconvert.exporters.pdf import PDFExporter
    import os
    if unknown_args is None:
        unknown_args = []
    if sargs.template:
        unknown_args = ['--template', os.path.abspath(sargs.template) if os.path.isfile(
            sargs.template) else sargs.template] + unknown_args
    # jupyter convert will add extension to output file...
    if output_file is not None and output_file.endswith('.pdf'):
        output_file = output_file[:-4]
    export_notebook(PDFExporter, 'pdf', notebook_file,
                    output_file, unknown_args)


def get_notebook_to_md_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.md (or --to md)',
                                     description='''Export Jupyter notebook with a SoS kernel to a
        markdown file. Additional command line arguments are passed directly to
        command "jupyter nbconvert --to markdown" so please refer to nbconvert manual for
        available options.''')
    return parser


def notebook_to_md(notebook_file, output_file, sargs=None, unknown_args=None):
    from nbconvert.exporters.markdown import MarkdownExporter
    export_notebook(MarkdownExporter, 'markdown',
                    notebook_file, output_file, unknown_args)


def get_notebook_to_notebook_parser():
    parser = argparse.ArgumentParser('sos convert FILE.ipynb FILE.ipynb (or --to ipynb)',
                                     description='''Export a Jupyter notebook with a non-SoS kernel to a
        SoS notebook with SoS kernel. A SoS notebook will simply be copied to
        the destination file.''')
    parser.add_argument('--python3-to-sos', action='store_true',
                        help='''Convert python3 cells to SoS.''')
    parser.add_argument('--inplace', action='store_true',
                        help='''Overwrite input notebook with the output.''')
    return parser


def notebook_to_notebook(notebook_file, output_file, sargs=None, unknown_args=None):
    notebook = nbformat.read(notebook_file, nbformat.NO_CONVERT)
    # get the kernel of the notebook
    # this is like 'R', there is another 'display_name'
    lan_name = notebook['metadata']['kernelspec']['language']
    # this is like 'ir'
    kernel_name = notebook['metadata']['kernelspec']['name']
    if kernel_name == 'sos':
        # already a SoS notebook?
        if sargs.inplace:
            return
        if output_file:
            import shutil
            shutil.copy(notebook_file, output_file)
        else:
            with open(notebook_file) as nb:
                sys.stdout.write(nb.read())
        return
    # convert to?
    elif kernel_name == 'python3' and sargs.python3_to_sos:
        to_lan = 'SoS'
        to_kernel = 'sos'
    else:
        to_lan = lan_name
        to_kernel = kernel_name
    # write all cells
    #
    cells = []
    for cell in notebook.cells:
        if cell.cell_type == 'code':
            cell.metadata['kernel'] = to_lan
        cells.append(cell)
    #
    # create header
    nb = new_notebook(cells=cells,
                      metadata={
                          'kernelspec': {
                              "display_name": "SoS",
                              "language": "sos",
                              "name": "sos"
                          },
                          "language_info": {
                              "file_extension": ".sos",
                              "mimetype": "text/x-sos",
                              "name": "sos",
                              "pygments_lexer": "python",
                              'nbconvert_exporter': 'sos_notebook.converter.SoS_Exporter',
                          },
                          'sos': {
                              'kernels': [
                                  ['SoS', 'sos', '', '']] +
                              ([[to_lan, to_kernel, '', '']]
                               if to_lan != 'SoS' else []),
                              'default_kernel': to_lan
                          }
                      }
                      )

    if sargs.inplace:
        with open(notebook_file, 'w') as new_nb:
            nbformat.write(nb, new_nb, 4)
        env.logger.info(f'Jupyter notebook saved to {notebook_file}')
    elif not output_file:
        nbformat.write(nb, sys.stdout, 4)
    else:
        with open(output_file, 'w') as new_nb:
            nbformat.write(nb, new_nb, 4)
        env.logger.info(f'Jupyter notebook saved to {output_file}')


def get_Rmarkdown_to_notebook_parser():
    parser = argparse.ArgumentParser('sos convert FILE.Rmd FILE.ipynb (or --to ipynb)',
                                     description='''Export a Rmarkdown file kernel to a SoS notebook. It currently
        only handles code block and Markdown, and not inline expression.''')
    return parser


def Rmarkdown_to_notebook(rmarkdown_file, output_file, sargs=None, unknown_args=None):
    #
    with open(rmarkdown_file) as script:
        content = script.read()
    #
    # identify the headers
    header = header = re.compile('^(#+\s.*$)', re.M)
    paragraphs = re.split(header, content)
    #
    cells = []
    cell_count = 1
    for idx, p in enumerate(paragraphs):
        if idx % 2 == 1:
            # this is header, let us create a markdown cell
            cells.append(
                new_markdown_cell(
                    source=p.strip()))
        else:
            # this is unknown yet, let us find ```{} block
            code = re.compile('^\s*(```{.*})$', re.M)
            endcode = re.compile('^\s*```$', re.M)

            for pidx, pc in enumerate(re.split(code, p)):
                if pidx == 0:
                    # piece before first code block. it might contain
                    # inline expression
                    cells.append(
                        new_markdown_cell(
                            source=pc.strip())
                    )
                elif pidx % 2 == 0:
                    # this is AFTER the {r} piece, let us assume all R code
                    # for now
                    # this is code, but it should end somewhere
                    pieces = re.split(endcode, pc)
                    # I belive that we should have
                    #   pieces[0] <- code
                    #   pieces[1] <- rest...
                    # but I could be wrong.
                    cells.append(
                        new_code_cell(
                            source=pieces[0],
                            execution_count=cell_count,
                            metadata={'kernel': 'R'}
                        )
                    )
                    cell_count += 1
                    #
                    for piece in pieces[1:]:
                        cells.append(
                            new_markdown_cell(
                                source=piece.strip())
                        )
    #
    # create header
    nb = new_notebook(cells=cells,
                      metadata={
                          'kernelspec': {
                              "display_name": "SoS",
                              "language": "sos",
                              "name": "sos"
                          },
                          "language_info": {
                              "file_extension": ".sos",
                              "mimetype": "text/x-sos",
                              "name": "sos",
                              "pygments_lexer": "python",
                              'nbconvert_exporter': 'sos_notebook.converter.SoS_Exporter',
                          },
                          'sos': {
                              'kernels': [
                                  ['SoS', 'sos', '', ''],
                                  ['R', 'ir', '', '']],
                              'default_kernel': 'R'
                          }
                      }
                      )

    if not output_file:
        nbformat.write(nb, sys.stdout, 4)
    else:
        with open(output_file, 'w') as new_nb:
            nbformat.write(nb, new_nb, 4)
        env.logger.info(f'Jupyter notebook saved to {output_file}')

#!/usr/bin/env python3 # # Copyright (c) <NAME> and the University of Texas MD Anderson Cancer Center # Distributed under the terms of the 3-clause BSD License. # # Converter from Notebook # Export Jupyter notebook with a SoS kernel to a         .sos file. The cells are presented in the .sos file as         cell structure lines, which will be ignored if executed         in batch mode # This class cannot be defined in .kernel because it would cause some # weird problem with unittesting not able to resolve __main__ # in non-all mode, markdown cells are ignored because they can be mistakenly # treated as markdown content of an action or script #806 # # Non-sos code cells are also ignored # look retrospectively for comments # other content, namely non-%include lines before section header is ignored # Convert a ipython notebook to sos format. # # Converter to Notebook # Convert a sos script to Jupyter notebook (.ipynb)             so that it can be opened by Jupyter notebook. # if a section consist of all report, report it as a markdown cell #!, code cell assumed.') # # remove any trailing blank lines... # ID is dynamically generated by the frontend and does not exist # in the backend for batch mode # sos is the additional meta information sent to kernel # the reset is copied from https://github.com/jupyter/nbconvert/blob/master/nbconvert/preprocessors/execute.py # because we only need to change the first line #  msg_id = self.kc.execute(cell.source) # We've already waited for execute_reply, so all output # should already be waiting. However, on slow networks, like # in certain CI systems, waiting < 1 second might miss messages. # So long as the kernel sends a status:idle message when it # finishes, we won't actually have to wait this long, anyway. # not an output from our execution # set the prompt number for the input and the output # clear display_id mapping for this cell # update_display_data doesn't get recorded # record output index in: #   _display_id_map[display_id][cell_idx] #+ ', line): Convert a sos script to iPython notebook (.ipynb) so that it can be opened     by Jupyter notebook. #fileformat line.') # get ride of empty content # get ride of empty content # other cases # # # if err: #    raise RuntimeError(repr(err)) # # notebook to HTML # import os import sos import sos_notebook  c = get_config() c.TemplateExporter.template_path.extend([   os.path.join(os.path.split(os.path.abspath(sos.__file__))[0], 'templates'),   os.path.join(os.path.split(os.path.abspath(sos_notebook.__file__))[0], 'templates')]) # identify output files # allow browser some time to process the file before this process removes it Export Jupyter notebook with a SoS kernel to a         .html file. Additional command line arguments are passed directly to         command "jupyter nbconvert --to html" so please refer to nbconvert manual for         available options. Template to export Jupyter notebook with sos kernel. SoS provides a number         of templates, with sos-report displays markdown cells and only output of cells with         prominent tag, and a control panel to control the display of the rest of the content Execute the notebook in batch mode (as if running "Cell -> Run All"                           from Jupyter notebook interface before converting to HTML Open the output file in a broswer. In case no html file is specified,         this option will display the HTML file in a browser, instead of writing its         content to standard output. # the step can take long time to complete Export Jupyter notebook with a SoS kernel to a         .pdf file. Additional command line arguments are passed directly to         command "jupyter nbconvert --to pdf" so please refer to nbconvert manual for         available options. Template to export Jupyter notebook with sos kernel. SoS provides a number         of templates, with sos-report displays markdown cells and only output of cells with         prominent tag, and a control panel to control the display of the rest of the content # jupyter convert will add extension to output file... Export Jupyter notebook with a SoS kernel to a         markdown file. Additional command line arguments are passed directly to         command "jupyter nbconvert --to markdown" so please refer to nbconvert manual for         available options. Export a Jupyter notebook with a non-SoS kernel to a         SoS notebook with SoS kernel. A SoS notebook will simply be copied to         the destination file. Convert python3 cells to SoS. Overwrite input notebook with the output. # get the kernel of the notebook # this is like 'R', there is another 'display_name' # this is like 'ir' # already a SoS notebook? # convert to? # write all cells # # # create header Export a Rmarkdown file kernel to a SoS notebook. It currently         only handles code block and Markdown, and not inline expression. # # # identify the headers #+\s.*$)', re.M) # # this is header, let us create a markdown cell # this is unknown yet, let us find ```{} block # piece before first code block. it might contain # inline expression # this is AFTER the {r} piece, let us assume all R code # for now # this is code, but it should end somewhere # I belive that we should have #   pieces[0] <- code #   pieces[1] <- rest... # but I could be wrong. # # # create header