matthewfeickert

Scientific open source software I've contributed to

This is an incomplete list that focuses only on software that is widely used to some extent.

This Gist is motivated by [Michael Zingale][Micahel GitHub]'s (@zingale) idea of an ["open source passport"][open source passport tweet]. This is not meant to be a prototype, but just a list until such a project gets made.

• pyhf
• cabinetry
• hist
• mplhep

matthewfeickert

Use a CVMFS LCG view hybrid Python virtual environment for HTCondor submissions

Create virtual environment

Generate a Python virtual environment using the Python runtime provided by a LCG view, and then from a high level requirements.txt file use pip-tools to compile an environment given by the accompanying lock file.

$ bash create_cvmfs_venv.sh

matthewfeickert

Summary of fixed POI problem for WSMaker to pyhf translation

It is desirable to be able to take a workspace created with WSMaker and use pyhf's translation utilities to write out a HistFactory JSON workspace file that is a pyhf compatible format. This is possible, however, when this happens the workspace has the POI fixed, which then makes statistical inference impossible.

Example

JC has shared with us one of his WSMaker workspaces that he's generated

$ tree -L 1 output/SemileptonicVBS_mc16ade_v3312_1LepOnly.1lepResBooRNNNoFid_m5_p0_SemileptonicVBS_13TeV_Systs_FS0_0_1lepResBooRNNNoFid_m5_p0/

matthewfeickert

mplhep styles with contourf log scale causes hang

I'm trying to do an interpolation of some points on a grid with mplhep v0.3.21 for an analysis at the moment. However, if I try to use matplotlib.pyplot.contourf with log spaces color levels using mplhep will cause a warning along the lines of

# Locator attempting to generate 18497 ticks ([0.15405694150420948, ..., 999.9912470033628]), which exceeds Locator.MAXTICKS (1000).

and it will then hang (I don't know if it resolves, as I kill it with a KeyboardInterrupt when it is clear it won't finish in a second or so).

matthewfeickert

Advice for Open Source Maintainers

Collections of examples of how to deal with the multi-hat aspects of being a maintainer of an open source project.

Code of Conduct Issues

Refusal to accept Code of Conduct

• setuptools Issue 3305

matthewfeickert

ARG BASE_IMAGE=python:3.9-slim-bullseye
FROM ${BASE_IMAGE} as base

SHELL [ "/bin/bash", "-c" ]

COPY packages.txt packages.txt
# Set PATH to pickup virtualenv by default
ENV PATH=/usr/local/venv/bin:"${PATH}"
RUN apt-get -qq -y update && \
    DEBIAN_FRONTEND=noninteractive apt-get -qq -y install --no-install-recommends $(cat packages.txt) && \

matthewfeickert

Floating point deviation in jax.numpy.percentile with linear interpolation between v0.2.20 and v0.2.21

Hi. There is some (very minor) deviations in the output of jax.numpy.percentile between jax v0.2.20 and v0.2.21 in the case that linear interpolation is used (the default). Interestingly, it is really in jax.numpy.percentile and not in jax.numpy.quantile as can be shown in the included example (for convenience this Issue also exists as a GitHub Gist).

Minimal failing example

# example.py
import jax
import jax.numpy as jnp

matthewfeickert

PyTorch Geometric Setup on DGX

Steps

1. Create a Python virtual enviroment and activate it

[user@hal-dgx]$ pyenv virtualenv 3.9.6 pytorch-geometric-example
[user@hal-dgx]$ pyenv activate pytorch-geometric-example
(pytorch-geometric-example) [user@hal-dgx]$ python -m pip install --upgrade pip setuptools wheel

matthewfeickert

Simple cProfile example with snakeviz

Environment Setup

Make a Python virtual environment and install the dependencies

python -m pip install --upgrade pip setuptools wheel
python -m pip install -r requirements.txt

matthewfeickert

If you enclose a regex in parentheses () whatever is enclosed can be used in a search and replace by a number that is indexed starting with 1. So for example

\section{\sc Research Interests}

can be found with the regex