code: def nbcompile(workdir, fileroot, html=True, basenb='', agdir=''):
      
  
      from shutil import copy
      from rtpipe import get_notebook
      from subprocess import call
  
      os.environ['fileroot'] = fileroot
      if agdir:
          os.environ['agdir'] = agdir
  
      if not basenb:
          basenb = get_notebook('baseinteract.ipynb')
  
      logger.info('Moving to {0} and building notebook for {1}'.format(workdir, fileroot))
      os.chdir(workdir)
      copy(basenb, '{0}/{1}.ipynb'.format(workdir, fileroot))
  
      cmd = 'jupyter nbconvert {0}.ipynb --inplace --execute --to notebook --allow-errors --ExecutePreprocessor.timeout=3600'.format(fileroot).split(' ')
      status = call(cmd)
  
      cmd = 'jupyter trust {0}.ipynb'.format(fileroot).split(' ')
      status = call(cmd)
  
      if html:
          cmd = 'jupyter nbconvert {0}.ipynb --to html --output {0}.html'.format(fileroot).split(' ')
          status = call(cmd)
docs: Run analysis pipeline from jupyter base notebook and save as notebook and html.
  
      html will also compile static html version
      basenb can be provided, else will get distributed version.
      agdir is the activegit repo (optional)