Tag Archives: python

Righter signatures in Jupyter

Did you know you can change the signature of functions dynamically in Python 3? It is a bit nasty, and maybe will make things look nicer for vivarium users.

Attempt: https://github.com/ihmeuw/vivarium/pull/2
Docs: https://docs.python.org/3/library/inspect.html#inspect.Signature
SO question that got me started: https://stackoverflow.com/a/33112180/1935494

Comments Off on Righter signatures in Jupyter

Filed under Uncategorized

Introducing Vivarium

I’ve had a new line of research developing for the last 18 months or so—*microsimulation*. It started when I stepped in to help with the “Cost Effectiveness Analysis with Microsimulation” (or CEAM) project at IHME. Now it is growing and growing to take over all of my research and recreation time. Is that bad or good?

Some of this work has now seen daylight from our presentations at SummerSim and iHEA in July, and today I am please to introduce a python package that you can use, too.

The programmers I’ve been working with on this convinced me that it is not just for cost effectiveness analysis and we need a more expansive name for it. So I present to you: vivarium. https://github.com/ihmeuw/vivarium


Filed under Uncategorized

Infographics in Python: Plot a Noun Project Icon on a Matplotlib Chart

I had to put an icon on a chart in Python last week, and I couldn’t find a good brief blog about how to do it. Here is what I cobbled together:

1. Find a free, appropriate image from The Noun Project.
2. Load it into Python with plt.imread
3. Draw it in the proper place on a figure with plt.imshow and some cryptic, hacky options.

Looks good, right?

See this all in action here: https://gist.github.com/aflaxman/c171050384471636e8f23f322ba7e9c5

Comments Off on Infographics in Python: Plot a Noun Project Icon on a Matplotlib Chart

Filed under dataviz

So cool–nbtutor

The first release of nbtutor (“Visualize Python code execution (line-by-line) in Jupyter Notebook cells.”) is available on pypi:

pip install nbtutor
jupyter nbextension install --sys-prefix --overwrite --py nbtutor
jupyter nbextension enable --sys-prefix --py nbtutor


Comments Off on So cool–nbtutor

Filed under education

dfply package

Potentially of interest, although I’ve done enough d3js to think that .select .head is fine notation:

dfply Version: 0.2.4

GitHub – kieferk from November 28, 2016
“The dfply package makes it possible to do R’s dplyr-style data manipulation with pipes in python on pandas DataFrames.”

from dfply import *

diamonds >> select(X.carat, X.cut) >> head(3)

   carat      cut
0   0.23    Ideal
1   0.21  Premium
2   0.23     Good

Comments Off on dfply package

Filed under software engineering

py.test recipes for slowness

Useful material on how to deal with slow tests in py.test, a bit buried in the docs:

From http://doc.pytest.org/en/latest/usage.html, to get a list of the slowest 10 test durations:

pytest --durations=10

From http://doc.pytest.org/en/latest/example/simple.html, to skip slow tests unless they are requested:

# content of conftest.py

import pytest
def pytest_addoption(parser):
    parser.addoption("--runslow", action="store_true",
        help="run slow tests")

# content of test_module.py
import pytest

slow = pytest.mark.skipif(
    not pytest.config.getoption("--runslow"),
    reason="need --runslow option to run"

def test_func_fast():

def test_func_slow():

Very convenient to know.

Comments Off on py.test recipes for slowness

Filed under software engineering

Delta Time in Python: Simple calendar times with Pandas

Here is something that Google did not help with as quickly as I would have expected: how do I convert start and stop times into the time between events in seconds (or minutes)?

Or for the busy searcher “how do I convert Pandas Timedelta to seconds”?

The classy answer is:

start_time = df.interviewstarttime.map(pd.Timestamp)
end_time = df.interviewendtime.map(pd.Timestamp)

((end_time-start_time) / pd.Timedelta(minutes=1)).describe()

I found it hidden away here: http://www.datasciencebytes.com/bytes/2015/05/16/pandas-timedelta-histograms-unit-conversion-and-overflow-danger/


Filed under statistics