Using pweave module

Pweave can also be used as module from the Python interpreter. This has some advantages over just using the scripts. First the execution of the code will be faster because all modules all already imported. It is also possible to fully customize the document execution and formatting using the Pweb class.

pweave module contains two functions weave() and tangle() that offer the same functionality as the command line scripts.

Simple weaving and tangling:

Here’s and example of simple weaving and tangling using example document ma.mdw. Notice that pweave prints out the progress so in case of an error you can tell in which chunk it occurred.

import pweave
# Weave a pandoc document with default options
pweave.weave('ma.mdw', doctype = "pandoc")

---------------------------------------------------------------------------FileNotFoundError
Traceback (most recent call last)~/anaconda3/lib/python3.6/site-
packages/pweave/readers.py in read_file_or_url(source)
     15     try:
---> 16         codefile = io.open(source, 'r', encoding='utf-8')
     17         contents = codefile.read()
FileNotFoundError: [Errno 2] No such file or directory: 'ma.mdw'
During handling of the above exception, another exception occurred:
ValueError                                Traceback (most recent call
last)<ipython-input-1-00fa7e3b1899> in <module>()
      1 import pweave
      2 # Weave a pandoc document with default options
----> 3 pweave.weave('ma.mdw', doctype = "pandoc")
~/anaconda3/lib/python3.6/site-packages/pweave/__init__.py in
weave(file, doctype, informat, kernel, plot, docmode, cache, figdir,
cachedir, figformat, listformats, output, mimetype)
     49     doc = Pweb(file, informat=informat, doctype=doctype,
     50                kernel=kernel, output=output, figdir=figdir,
---> 51                mimetype=mimetype
     52                )
     53     doc.documentationmode = docmode
~/anaconda3/lib/python3.6/site-packages/pweave/pweb.py in
__init__(self, source, doctype, informat, kernel, output, figdir,
mimetype)
     68
     69         self.setformat(doctype)
---> 70         self.read(reader = informat)
     71
     72     def _setwd(self):
~/anaconda3/lib/python3.6/site-packages/pweave/pweb.py in read(self,
string, basename, reader)
    106
    107         if string is None:
--> 108             self.reader = Reader(file=self.source)
    109         else:
    110             self.reader = self.Reader(string=string)
~/anaconda3/lib/python3.6/site-packages/pweave/readers.py in
__init__(self, file, string)
     36         # Get input from string or
     37         if file is not None:
---> 38             self.rawtext = read_file_or_url(self.source)
     39         else:
     40             self.rawtext = string
~/anaconda3/lib/python3.6/site-packages/pweave/readers.py in
read_file_or_url(source)
     18         codefile.close()
     19     except IOError:
---> 20         r = request.urlopen(source)
     21         contents = r.read().decode("utf-8")
     22         r.close()
~/anaconda3/lib/python3.6/urllib/request.py in urlopen(url, data,
timeout, cafile, capath, cadefault, context)
    221     else:
    222         opener = _opener
--> 223     return opener.open(url, data, timeout)
    224
    225 def install_opener(opener):
~/anaconda3/lib/python3.6/urllib/request.py in open(self, fullurl,
data, timeout)
    509         # accept a URL or a Request object
    510         if isinstance(fullurl, str):
--> 511             req = Request(fullurl, data)
    512         else:
    513             req = fullurl
~/anaconda3/lib/python3.6/urllib/request.py in __init__(self, url,
data, headers, origin_req_host, unverifiable, method)
    327                  origin_req_host=None, unverifiable=False,
    328                  method=None):
--> 329         self.full_url = url
    330         self.headers = {}
    331         self.unredirected_hdrs = {}
~/anaconda3/lib/python3.6/urllib/request.py in full_url(self, url)
    353         self._full_url = unwrap(url)
    354         self._full_url, self.fragment =
splittag(self._full_url)
--> 355         self._parse()
    356
    357     @full_url.deleter
~/anaconda3/lib/python3.6/urllib/request.py in _parse(self)
    382         self.type, rest = splittype(self._full_url)
    383         if self.type is None:
--> 384             raise ValueError("unknown url type: %r" %
self.full_url)
    385         self.host, self.selector = splithost(rest)
    386         if self.host:
ValueError: unknown url type: 'ma.mdw'

# Extract the code
pweave.tangle('ma.mdw')

---------------------------------------------------------------------------AttributeError
Traceback (most recent call last)<ipython-input-1-d41c1a734f25> in
<module>()
      1 # Extract the code
----> 2 pweave.tangle('ma.mdw')
~/anaconda3/lib/python3.6/site-packages/pweave/__init__.py in
tangle(file, informat)
     64     :param file: ``string`` the pweave document containing the
code
     65     """
---> 66     doc = Pweb(file, kernel = None, informat = informat)
     67     doc.tangle()
     68
~/anaconda3/lib/python3.6/site-packages/pweave/pweb.py in
__init__(self, source, doctype, informat, kernel, output, figdir,
mimetype)
     67         self.theme = "skeleton"
     68
---> 69         self.setformat(doctype)
     70         self.read(reader = informat)
     71
~/anaconda3/lib/python3.6/site-packages/pweave/pweb.py in
setformat(self, doctype, Formatter)
    148
    149         self.formatter = Formatter([],
--> 150                                    kernel = self.kernel,
    151                                    language = self.language,
    152                                    mimetype =
self.mimetype.type,
AttributeError: 'Pweb' object has no attribute 'kernel'

Pweave function reference

pweave.weave(file, doctype=None, informat=None, kernel='python3', plot=True, docmode=False, cache=False, figdir='figures', cachedir='cache', figformat=None, listformats=False, output=None, mimetype=None)

Processes a Pweave document and writes output to a file

Parameters:

• file – string input file
• doctype – string output document format: call with listformats true to get list of supported formats.
• informat – string input format: “noweb”, “markdown”, “notebook” or “script”
• kernel – string Jupyter kernel used to run code: default is python3
• plot – bool use matplotlib
• docmode – bool use documentation mode, chunk code and results will be loaded from cache and inline code will be hidden
• cache – bool Cache results to disk for documentation mode
• figdir – string directory path for figures
• cachedir – string directory path for cached results used in documentation mode
• figformat – string format for saved figures (e.g. ‘.png’), if None then the default for each format is used
• listformats – bool List available formats and exit
• output – string output file
• mimetype – string Source document’s text mimetype. This is used to set cell type in Jupyter notebooks.

pweave.tangle(file, informat=None)

Tangles a noweb file i.e. extracts code from code chunks to a .py file

Parameters:file – string the pweave document containing the code

pweave.publish(file, doc_format='html', theme='skeleton', latex_engine='pdflatex', output=None)

Publish python script and results to html or pdf, expects that doc chunks are written in markdown.

Parameters:

• file – string input file”
• format – string output format “html” of “pdf”, pdf output requires pandoc and pdflatex in your path.
• latex_engine – string the command for running latex. Defaults to “pdflatex”.
• output – string output file. Use .tex extension for pdf output.

pweave.convert(file, informat='noweb', outformat='script', pandoc_args=None, listformats=False)

Convert input file from script to noweb or vice versa

Parameters:

• file – string input file
• informat – string input format noweb, script or notebook
• outformat – string input format noweb or script
• pandoc_args – string arguments passed to pandoc to convert doc chunks. e.g. to convert from markdown to latex use: “-f markdown -t latex” . Note that each doc chunk is converted separately so you can’t use pandocs -s option.
• listformats – bool List available formats and exit

pweave.spin(file)

Convert input file from script format to noweb format, similar to Knitr’s spin.

More options with Pweb Class

Weaving, tangling and pweave options are implemented using Pweb class. There is an example about customizations and the class reference is below.

Pweb Class

class pweave.Pweb(source, doctype=None, *, informat=None, kernel='python3', output=None, figdir='figures', mimetype=None)

Process a Pweave document

Parameters:

• source – string name of the input document.
• doctype – string output format.
• informat – string input format
• kernel – string name of jupyter kernel used to run code
• output – string output path
• figdir – string figure directory
• mimetype – Source document’s text mimetype. This is used to set cell type in Jupyter notebooks

documentationmode = None

Use documentation mode

format()

Format executed code for writing.

getformat()

Get current format dictionary. See: http://mpastell.com/pweave/customizing.html

read(string=None, basename='string_input', reader=None)

Parse document

Param:None (set automatically), reader name or class object

run(Processor=None)

Execute code in the document

setformat(doctype=None, Formatter=None)

Set formatter by name or class. You can pass either

Parameters:

• doctype – The name of Pweave output format
• Formatter – Formatter class

setkernel(kernel)

Set the kernel for jupyter_client

tangle()

Tangle the document

updateformat(dict)

Update existing format, See: http://mpastell.com/pweave/customizing.html

weave()

Weave the document, equals -> parse, run, format, write

write()

Write formatted code to file