Author Archives: Alice Allen

WE20211204: This week in the ASCL

It was a loud week at ASCL Central, what with a backhoe and a couple of Bobcats working outside, so I decamped to my office at UMD for a couple of days to get away from the noise and, especially, the diesel exhaust. It was also a productive week, with eighteen entries added to the ASCL, two records curated, and notification emails sent out. I submitted my proceedings paper for ADASS. A paper submitted in September came back from review, and we’ve started a series of writing sprints to address the reviewers’ concerns; the paper will be resubmitted before the end of the year. I also did some organizing work to prepare for this coming week’s FORCE2021 Hackathons; the SciCodes consortium hopes to make progress on several items during this event, which will be held on Monday and Friday. Come join us!

A very muddy backyard with a backhoe in it

In the dawn’s early light, a lot of mud.

November 2021 additions to the ASCL

Eighteen codes were added to the ASCL in November:

astroDDPM: Realistic galaxy simulation via score-based generative models
Astrosat: Satellite transit calculator
CEvNS: Calculate Coherent Elastic Neutrino-Nucleus Scattering cross sections and recoil spectra
COCOPLOT: COlor COllapsed PLOTting software
CoLoRe: Cosmological Lofty Realization
flatstar: Make 2d intensity maps of limb-darkened stars

gCMCRT: 3D Monte Carlo Radiative Transfer for exoplanet atmospheres using GPUs
GWToolbox: Gravitational wave observation simulator
JAX: Autograd and XLA
LEGWORK: LISA Evolution and Gravitational Wave ORbit Kit
Nii: Multidimensional posterior distributions framework
NLopt: Nonlinear optimization library

p-winds: Python implementation of Parker wind models for planetary atmospheres
prose: FITS images processing pipeline
PSwarm: Global optimization solver for bound and linear constrained problems
pySYD: Measuring global asteroseismic parameters
SteParSyn: Stellar atmospheric parameters using the spectral synthesis method
UniMAP: Unicorn Multi-window Anomaly Detection Pipeline

Citation method, please? A case study in astrophysics

I did an experiment last year to see whether I could influence software authors to add either CITATION.cff or codemeta.json files to their repos to make clear how the software should be cited. It mostly didn’t work, but was still a useful exercise. I’ve written a short paper about it that will appear on arXiv tonight (ETA: here) and is available now at the link below.

Abstract: Software citation has accelerated in astrophysics in the past decade, resulting in the field now having multiple trackable ways to cite computational methods. Yet most software authors do not specify how they would like their code to be cited, while others specify a citation method that is not easily tracked (or tracked at all) by most indexers. Two metadata file formats, codemeta.json and CITATION.cff, developed in 2016 and 2017 respectively, are useful for specifying how software should be cited. In 2020, the Astrophysics Source Code Library (ASCL, undertook a year-long effort to generate and send these software metadata files, specific to each computational method, to code authors for editing and inclusion on their code sites. We wanted to answer the question, “Would sending these files to software authors increase adoption of one, the other, or both of these metadata files?” The answer
in this case was no. Furthermore, only 41% of the 135 code sites examined for use of these files had citation information in any form available. The lack of such information creates an obstacle for article authors to provide credit to software creators, thus hindering citation of and recognition for computational contributions to research and the scientists who develop and maintain software.

Citation method, please? A case study in astrophysics (PDF)

WE20211113: This week in the ASCL

A busy week, but more on the organizing and writing side than actual work on the ASCL itself. One of the organizational tasks was for a Deep Dive webinar on software citation for FORCE2021; this is a dedicated session presented by the FORCE11 Software Citation Implementation Working Group (SCIWG), and will be held on Tuesday, December 7 at 17:00 UTC. Several lightning talks will be presented on the work of the SCIWG, what challenges still exist, and work that is planned in the future, and then the floor will be opened for discussion among presenters and attendees. I wrote a first draft (which I expect is pretty close to the final draft) of a proceedings paper for last month’s ADASS meeting, this for the poster I presented. By “wrote,” I mean “mostly fought with LaTeX,” since that struggle took the majority of the time spent on the paper. On the ASCL itself, seven entries were curated and three new entries were staged.

WE20211106: This week in the ASCL

This past week, fourteen new code entries were put into production, fourteen entries were curated, and three entries were staged. We also sent numerous emails to code authors. We’ve been working on increasing the number of codes added every month, and that effort is paying off, as you can see in the graph (from our dashboard) below. In 2017-2020, we averaged 21 codes/month; this year so far, we’re averaging almost 28 new entries/month.

histogram showing number of codes added each year, with the column for 2021 showing an increase over the previous three years

We currently provide all of our public data in JSON and individual entries in both CITATION.cff and codemeta.json. This past week, we had some discussion with one of our developers about making all of our public data available in codemeta.json. We don’t have a date for doing this yet, but perhaps will make this change in time for the January AAS meeting.

October 2021 additions to the ASCL

Twenty-two codes were added to the ASCL in October:

ArtPop: Artificial Stellar Populations generator
BASTA: BAyesian STellar Algorithm
BCES: Linear regression for data with measurement errors and intrinsic scatter
exodetbox: Finding planet-star projected separation extrema and difference in magnitude extrema
FEniCS: Computing platform for solving partial differential equations

Flux: Julia machine learning library
GGCHEMPY: Gas-Grain CHEMical code for interstellar medium in Python3
GRASS: GRanulation and Spectrum Simulator
JWSTSim: Geometric-Focused JWST Deep Field Image Simulation
Nauyaca: N-body approach for determining planetary masses and orbital elements

ParSNIP: Parametrization of SuperNova Intrinsic Properties
PISCOLA: Python for Intelligent Supernova-COsmology Light-curve Analysis
PSRDADA: Distributed Acquisition and Data Analysis for Radio Astronomy
PT-REX: Point-to-point TRend EXtractor
pyro: Deep universal probabilistic programming with Python and PyTorch

Quokka: Two-moment AMR radiation hydrodynamics on GPUs for astrophysics
SELCIE: Screening Equations Linearly Constructed and Iteratively Evaluated
swordfish: Information yield of counting experiments
TauRunner: Code to propagate tau neutrinos at very high energies
ThERESA: 3D Exoplanet Cartography

TULIPS: Tool for Understanding the Lives, Interiors, and Physics of Stars
XookSuut: Model circular and noncircular flows on 2D velocity maps

WE20211030: This week in the ASCL

The ADASS conference took place this week. The ASCL presented a poster about SciCodes at the conference. Though ADASS took up most of my time, eight new code entries, three of them submitted by their authors, were assigned ASCL IDs and moved into production. I also wrote and submitted an abstract for an iPoster presentation at the AAS’s January 2022 meeting.

ASCL poster on SciCodes consortium at ADASS XXXI

Poster describing the SciCodes consortium and how it might be of interest to astronomers

The Astrophysics Source Code Library (ASCL, started in 1999, is a free open registry of software used in refereed astronomy research. Over the past few years, it has spearheaded an effort to form a consortium of scientific software registries and repositories. In 2019 and 2020, ASCL contacted editors and maintainers of academic discipline and institutional software registries and repositories in math, biology, neuroscience, geophysics, remote sensing, and other fields to develop a list of best practices for research software registries and repositories. At the completion of that project, performed as a Task Force for a FORCE11 working group, members decided to form SciCodes as an ongoing consortium. This poster will cover the consortium’s work so far, what it is currently working on, what it hopes to achieve for making scientific research software more discoverable across disciplines, and how the consortium can benefit astronomers.

Download poster (PDF)


WE20211023: This week in the ASCL

This was the week before ADASS! The meeting this year is a hybrid meeting, with some attendees in Cape Town, and the others scattered all over the world. As much as I would love to be in Cape Town, I am attending virtually because of the pandemic. My poster this year involves but isn’t about the ASCL; instead, I’m presenting a poster about SciCodes.

Speaking of SciCodes, this week was our monthly meetings, so I spent time on them, but also had time for working on the ASCL. Random code of the day posts were scheduled through the end of the month and twenty entries were updated. Six new codes were staged, and two were submitted. This coming week, numerous ASCL-involved folks will be at ADASS, and I look forward to seeing them there!

WE20211016: This week in the ASCL

Writing and organizing seemed to be this week’s theme. Melissa Harrison and I wrote and submitted a proposal for a dedicated working group session at FORCE2021 on behalf of the FORCE11 Software Citation Implementation Working Group and secured a number of speakers for lightning talks. I got a rejection notice on Wednesday for a paper I’d submitted in early September; based on feedback from the reviewers and the to-do list I’d started after submitting it, I edited the paper, intending to post it to arXiv. A couple of people encouraged me to submit it to another journal, however, so I did. I also worked on my ADASS poster and paper. Actual work on the ASCL itself included curating seven entries, processing one submission and assigning the code an ASCL ID, and staging three new entries.