Linting non-inclusive language with blocklint

Blocklint is a simple command line utility for finding non-inclusive wording with an emphasis on source code. If you’ve used a modern IDE, you know the importance of immediate feedback for compilation errors or even stylistic slip-ups.  Knowing all variables should be declared or that lines must be less than 80 characters long is good, but adhering to those rules takes a back seat when in the flow of writing code.  A linter brings these issues back into your consciousness by highlighting the problematic lines of code.  Over time, the enforced style becomes more intuitive but the linter is always there to nudge you if you slip.

Continue reading

Monitoring slurm efficiency with reportseff


As I started using Snakemake, I had hundreds of jobs that I wanted to get performance information about. seff gives the efficiency information I wanted, but for only a single job at a time. sacct handles multiple jobs, but couldn’t give the efficiency. With the current python implementation of reportseff, all job information is obtained from a single sacct call and with click the output is colored to quickly see how things are running.

Continue reading

Boost Histogram 0.6

boost-histogram logo

The foundational histogramming package for Python, boost-histogram, was just updated to version 0.6! This is a major update to the new Boost.Histogram bindings. Version 0.6.1 is based on the recently released Boost C++ Libraries version 1.72 Histogram package.

This Python library is part of a larger picture in the Scikit-HEP ecosystem of tools for Particle Physics and is funded by DIANA/HEP and IRIS-HEP. It is the core library for making and manipulating histograms. Other packages are under development to provide a complete set of tools to work with and visualize histograms. The Aghast package is designed to convert between popular histogram formats, and the Hist package will be designed to make common analysis tasks simple, like plotting via tools such as the mplhep package. Hist and Aghast will be initially driven by HEP (High Energy Physics and Particle Physics) needs, but outside issues and contributions are welcome and encouraged.

Continue reading on ISciNumPy →

Configuration settings in the ASPIRE package

As with any substantial application package, the ASPIRE project needed a convenient way to specify configuration settings pertaining to different parts of the computational pipeline.

What follows below are some outlines from our attempts to tackle this configuration issue. Where a supplementary (and hopefully useful) nugget is provided, or a caveat discussed, I shall append a linked numeral, like so: (n)

A brief background of ASPIRE

ASPIRE is a Python (3.6) package under development, which ingests Micrographs, the output of Cryo-Electron Microscopy (images that closely resemble television static), and comes up with a 3D reconstruction of the molecule. Read the excellent writeup on the ASPIRE page for a more comprehensive review of the package.

Continue reading