Knitpy Overview

knitpy: dynamic report generation with
python
Jan Schulz
12.03.2015
This is a port of knitr (http://yihui.name/knitr/) and rmarkdown
(http://rmarkdown.rstudio.com/) to python.
For a complete description of the code format see
http://rmarkdown.rstudio.com/ and replace {r...} by {python ...} and of
course use python code blocks
Examples
Here are some examples:
print("Execute some code chunk and show the result")
## Execute some code chunk and show the result
Codechunks which contain lines without output (e.g. assign the result
or comments) will be shown in the same code block:
# A comment
text = "All code in the same code block until some output is produced..."
more_text = "...and some more."
print(text)
## All code in the same code block until some output is produced...
print(more_text)
## ...and some more.
Code chunk arguments

You can use different arguments in the codechunk declaration. Using
echo=False will not show the code but only the result.
## Only the output will be visible as `echo=False`
The next paragraphs explores the code chunk argument results.

If hide, knitpy will not display the codes results in the final document.
If hold, knitpy will delay displaying all output pieces until the end of
the chunk. If asis, knitpy will pass through results without
reformatting them (useful if results return raw HTML, etc.)
results='hold' is not yet implemented.

print("Only the input is displayed, not the output")
## This is formatted as markdown:
## **This text** will be bold...
This text will be bold

Note: with python code it is recommended to use the IPython/Jupyter
display system and an appropriate wrapper (see below) to display such
output and not results="asis". This makes it possible to convert such
output if the output cant be included in the final format.
You can also not show codeblocks at all, but they will be run (not
included codeblock sets have_run = True):
if have_run == True:
print("'have_run==True': ran the codeblock before this one.")
## 'have_run==True': ran the codeblock before this one.
Using eval=False, one can prevent the evaluation of the codechunk

x=1
x += 1 # this is not executed as eval is False
x # still 1
## 1
To remove/hide a codechunk completely, i.e. neither execute it nor

show the code, you can use both eval=False, include=False: nothing will
be shown between this text
x += 1 # this is not executed and not even shown
and this text here!

The prefix in front of text output (per default ##) can be changed via
the comment chunk option to a different string or completely removed
by setting it to a empty string ""or None:
print("Text output")
# result: Text output
print("Text output")
Text output
Inline code
You can also include code inline: m=2 (expected: m=2)
IPython / Jupyter display framework

The display framework is also supported.
Plots will be included as images and included in the document. The
filename of the plot is derived from the chunk label (sinus in this
case). The code is not shown in this case (echo=False).
If a html or similar thing is displayed via the IPython display

framework, it will be included as is, meaning that apart from
text/plain-only output, everything else will be included without marking
it up as output. Knitpy automagically tries to include only formats
which are understood by pandoc and the final output format (in some
case converting the format to one which the final output can handle).
from IPython.core.display import display, HTML
display(HTML("<strong>strong text</strong>"))
strong text
It even handles pandas.DataFrames (be aware that not all formatting
can be converted into all output formats):
import pandas as pd
pd.set_option("display.width", 200)
s = """This is longer text"""
df = pd.DataFrame({"a":[1,2,3,4,5],"b":[s,"b","c",s,"e"]})
df
0
1
2
3
4
pandas.DataFrame can be represented as text/plain or text/html, but will
default to the html version. To force plain text, use either print(df) or set
the right pandas option:
pd.set_option("display.notebook_repr_html", False)
df
##
##
##
##
##
##
0
1
2
3
4
a
b
1 This is longer text
2
b
3
c
4 This is longer text
5
e
# set back the display

pd.set_option("display.notebook_repr_html", True)
You can also use package like tabulate together with results="asis" or
by wrapping it with the appropriate display class:
from tabulate import tabulate
from IPython.core.display import Markdown
# either print and use `results="asis"`
print(tabulate(df, list(df.columns), tablefmt="simple"))
0
1
2
3
4
# or use the IPython display framework to publish markdown
Markdown(tabulate(df, list(df.columns), tablefmt="simple"))
0
1
2
3
4
Note that the second version (wrapping it in Markdown) is preferred, as
this marks the output with the right mimetype and therefore can be
convertedif thats neededto something which the output format
understands!
Unfortunately, html tables have to be tweaked for the final output
format as e.g. too width tables spill over the page margin in PDF.
Error handling
Errors in code are shown with a bold error text:
import sys
print(sys.not_available)
ERROR: AttributeError: module object has no attribute not_available

AttributeError
Traceback (most recent call last)
<ipython-input-37-a5971246c0f7> in <module>()
----> 1 print(sys.not_available)
AttributeError: 'module' object has no attribute 'not_available'
for x in []:
print("No indention...")
ERROR: Code invalid

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What are some examples of code chunks shown?

How can code chunks be customized?

knitpy: dynamic report generation with

Code chunk arguments

The next paragraphs explores the code chunk argument results.

results='hold' is not yet implemented.

This text will be bold

Using eval=False, one can prevent the evaluation of the codechunk

To remove/hide a codechunk completely, i.e. neither execute it nor

and this text here!

IPython / Jupyter display framework

If a html or similar thing is displayed via the IPython display

# set back the display

ERROR: AttributeError: module object has no attribute not_available

ERROR: Code invalid

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