Category Archives: news

March 2021 additions to the ASCL

Thirty-one codes were added to the ASCL in March:

21cmDeepLearning: Matter density map extractor
ARTIS: 3D Monte Carlo radiative transfer code for supernovae
Astro-Fix: Correcting astronomical bad pixels in Python
AstroNet-Triage: Neural network for TESS light curve triage

AstroNet-Vetting: Neural network for TESS light curve vetting
Carsus: Atomic database for astronomy
CARTA: Cube Analysis and Rendering Tool for Astronomy
CRIME: Cosmological Realizations for Intensity Mapping Experiments

DarkEmulator: Cosmological emulation code for halo clustering statistics
DIAPHANE: Library for radiation and neutrino transport in hydrodynamical simulations
DRAKE: Relic density in concrete models prediction
GalacticDNSMass: Bayesian inference determination of mass distribution of Galactic double neutron stars

GalLenspy: Reconstruction of mass profile in disc-like galaxies from the gravitational lensing effect
ggm: Gaussian gradient magnitude filtering of astronomical images
hfs_fit: Atomic emission spectral line hyperfine structure fitting
LPF: Real-time detection of transient sources in radio data streams

nestle: Nested sampling algorithms for evaluating Bayesian evidence
PION: Computational fluid-dynamics package for astrophysics
Pyedra: Python implementation for asteroid phase curve fitting
PyPion: Post-processing code for PION simulation data

QuickCBC: Rapid and reliable inference for binary mergers
RAiSERed: Analytic AGN model based code for radio-frequency redshifts
redshifts: Spectroscopic redshifts search tool
satcand: Orbital stability and tidal migration constraints for KOI exomoon candidates

schNell: Fast calculation of N_ell for GW anisotropies
Silo: Saving scientific data to binary disk files
spalipy: Detection-based astronomical image registration
SparseBLS: Box-Fitting Least Squares implementation for sparse data

SUPERNU: Radiative transfer code for explosive outflows using Monte Carlo methods
TFF: Template Fourier Fitting
TransitFit: Exoplanet transit fitting package for multi-telescope datasets

MTU Colloquium talk on Schrödinger’s code: Opening the computational box

On Thursday, March 18, I am giving the physics colloquium at Michigan Technological University (MTU), which has hosted the Astrophysics Source Code Library since the ASCL’s inception in 1999. Despite having worked on the ASCL for nearly eleven years, I’ve never been to MTU; though I wish the visit could be in person, the talk will be presented virtually over Zoom. The presentation abstract is below, as is a link to the slides and links for all of the citations and resources mentioned in the talk.

Abstract: Though computational methods are widely used in many disciplines, many researchers do not share the source code they develop, making it difficult to replicate and reuse the work. This presentation will cover the changing landscape that includes funders’ requirements, policy changes for existing journals, community resources, and more, that make it easy to release and archive codes to ensure they are available to support the research they enabled, improve the reproducibility of science, increase confidence in research, and meet new requirements made by funders and journals in many disciplines. It will also cover how the Astrophysics Source Code Library (ASCL), which has been working since 1999 to improve the transparency of research by registering open codes used in research, has made it possible for software to be cited as a first-order research object, and how researchers can garner credit for their codes by having them cited correctly and improve papers by including citations for the computational methods that enabled the research.

Slides (PDF)


Astronomy and Computing (A&C)
Computational Astrophysics and Cosmology (ComAC)
Computing and Software for Big Science
Computer Physics Communications (CPC)
Journal of Open Research Software (JORS)
Journal of Open Source Software (JOSS)

Change leaders and guidelines

CITATION file format (CFF)
FAIR principles
FORCE11/FORCE11 Software Citation Principles
Software Sustainability Institute
Working toward Sustainable Software for Science: Practice and Experiences (WSSSPE)

Social coding sites and archival services

DOE CODE; more information
Software Heritage

Other resources

arXiv/arXiv Next Generation
Software licensing resources | Licensing Astrophysics Codes special session at AAS 225
Papers with Code

Cited sources (in order of appearance)

Goble (2014)
Ince, Hatton, & Graham-Cumming (2012)
Allen, Teuben, & Ryan (2018)
Ryan, Allen, & Teuben (2019); Data and code
Collberg, Proebsting, & Warren (2014), PDF
Howison & Bullard (2016)
Mangul et al (2018)
Zorotovic, Schreiber, & Parsons (2014)
Smart (2018)
Neupane et al (2019); Vice article
Barba (2019)
DOE policy
DOE policy FAQ
NSF policy
Nature Portfolio policy
Science policy
AAS Journals policy

February 2021 additions to the ASCL

Thirty codes were added to the ASCL in February:

BALRoGO: Bayesian Astrometric Likelihood Recovery of Galactic Objects
binaryoffset: Detecting and correcting the binary offset effect in CCDs
CMasher: Scientific colormaps for making accessible, informative plots
DaMaSCUS-SUN: Dark Matter Simulation Code for Underground Scatterings – Sun Edition
EqTide: Equilibrium Tide calculations

extinction: Dust extinction laws
ForwardDiff: Forward mode automatic differentiation for Julia
GalRotpy: Parametrize the rotation curve and gravitational potential of disk-like galaxies
GLEAM: Galaxy Line Emission and Absorption Modeling
hardCORE: Exoplanet core radius fractions calculator

HUAYNO: Hierarchically split-Up AstrophYsical N-body sOlver N-body code
lensingGW: Lensing of gravitational waves
Lightbeam: Simulate light through weakly-guiding waveguides
mirkwood: SED modeling using machine learning
MOSAIC: Multipole operator generator for Fast Multipole Method operators

MST: Minimum Spanning Tree algorithm for identifying large-scale filaments
Multi_CLASS: Cross-tracer angular power spectra of number counts using CLASS
MUSE-PSFR: PSF reconstruction for MUSE WFM-AO mode
nway: Bayesian cross-matching of astronomical catalogs
OPUS: Interoperable access to analysis and simulation codes

Piff: PSFs In the Full FOV
Pixell: Rectangular pixel map manipulation and harmonic analysis library
polgraw-allsky: All-sky almost-monochromatic gravitational-wave pipeline
PyAutoFit: Classy probabilistic programming
PyFstat: Continuous gravitational-wave data analysis

RASSINE: Normalizing 1D stellar spectra
spinOS: SPectroscopic and INterferometric Orbital Solution finder
ThumbStack: Map and profile stacking pipeline
viscm: Analyzing colormaps and creating new colormaps
X-PSI: X-ray Pulse Simulation and Inference

January 2021 additions to the ASCL

Eighteen codes were added to the ASCL in January:

3LPT-init: Initial conditions with third-order Lagrangian perturbation for cosmological N-body simulations
apogee: Tools for APOGEE data
Avocado: Photometric classification of astronomical transients and variables with biased spectroscopic samples
BAYES-LOSVD: Bayesian framework for non-parametric extraction of the LOSVD
cFS: core Flight System

Curvit: Create light curves from UVIT data
DarpanX: X-ray reflectivity of multilayer mirrors
Eigentools: Tools for studying linear eigenvalue problems
EphemMatch: Ephemeris matching of DR25 TCEs, KOIs, and EBs for false positive identification
Mask galaxy: Machine learning pipeline for morphological segmentation of galaxies

Nigraha: Find and evaluate planet candidates from TESS light curves
Octo-Tiger: HPX parallelized 3-D hydrodynamic code for stellar mergers
ptemcee: A parallel-tempered version of emcee
pyUPMASK: Unsupervised clustering method for stellar clusters
PyXspec: Python interface to XSPEC spectral-fitting program

radiowinds: Radio Emission from Stellar Winds
stratsi: Stratified streaming instability
whereistheplanet: Predicting positions of directly imaged companions

The ASCL at the 237th meeting of the American Astronomical Society

It’s that time of year again, when astronomers’ hearts and wings turn to AAS for the winter AAS meeting. This year, however, the wings are virtual; like other conferences in this time of pandemic, the 237th meeting of the AAS is online. I’m very impressed with the online meeting space, which includes a conference center with different locations to visit, a virtual exhibit hall, an iPoster gallery, and many opportunities through Slack and thoughtfully-planned activities to enable and encourage interaction between attendees, exhibitors, and presenters, including the always great Open Mic event, a highlight of the winter meeting, on Wednesday evening.

Members of the ASCL are presenting two iPosters + (the “plus” is a short Zoom session about  the poster) and an oral presentation at this meeting.

On Monday, Siddha Mavuram, an UMD student hired to do development work for the ASCL for our NASA ADAP project, is doing an iPoster + presentation titled Come search the ASCL with our new API! I also have an iPoster + presentation on Monday called Life, the Universe and Everything… you ever wanted to know about the Astrophysics Source Code Library. Though our short talks, using our posters only as our visual aids, are on Monday, our posters are available all week.

On Tuesday, Peter Teuben is presenting results of our NASA ADAP project. Though Siddha is presenting part of the development work done for this project, Peter is sharing the overall results in his oral presentation Increasing the visibility of NASA astrophysics software through the ASCL, showing how this project has made it possible to search the ASCL and ADS for NASA software through the use of keywords and, on ADS, the doctype value software. You can see these results yourself on the ASCL and with an ADS search.

Because I very cleverly failed to realize that all the links I added to the slides for my iPoster wouldn’t work once I made those slides images (doh!), I provide a PDF of these slides for download below in which most, but alas not all, of the links work. Later this week, I’ll provide a full list of links in another post that will contain all of the resources and links the ASCL is presenting this week.

Slides for Alice’s ASCL iPoster slideshow (PDF)

December 2020 additions to the ASCL

Twenty-six codes were added to the ASCL in December:

BinaryStarSolver: Orbital elements of binary stars solver
BlackHawk: Black hole evaporation calculator
dolphin: Automated pipeline for lens modeling
DRAGraces: Reduction pipeline for GRACES spectra

EinsteinPy: General Relativity and gravitational physics problems solver
EOS: Equation of State for planetary impacts
getsf: Multi-scale, multi-wavelength sources and filaments extraction
HCGrid: Mapping non-uniform radio astronomy data onto a uniformly distributed grid

HydroCode1D: 1D finite volume code
LALSuite: LIGO Scientific Collaboration Algorithm Library Suite
LIFELINE: LIne proFiles in massivE coLliding wInd biNariEs
MADLens: Differentiable lensing simulator

Magritte: 3D radiative transfer library
MLC_ELGs: Machine Learning Classifiers for intermediate redshift Emission Line Galaxies
NSCG: NOIRLab Source Catalog Generator
Pomegranate: Probabilistic model builder

PyXel: Astronomical X-ray imaging data modeling
Robovetter: Automatic vetting of Threshold Crossing Events (TCEs)
seaborn: Statistical data visualization
sedop: Optimize discrete versions of common SEDs

Sengi: Interactive viewer for spectral outputs from stellar population synthesis models
SimCADO: Observations simulator for infrared telescopes and instruments
Skye: Excess clustering of transit times detection
SLIT: Sparse Lens Inversion Technique

SWIGLAL: Access LALSuite libraries with Python and Octave scripts
TRAN_K2: Planetary transit search

November 2020 additions to the ASCL

Thirty codes were added to the ASCL in November 2020:

ACStools: Python tools for Hubble Space Telescope Advanced Camera for Surveys data
AdaMet: Adaptive Metropolis for Bayesian analysis
ARES: Accelerated Reionization Era Simulations
CAPTURE: Interferometric pipeline for image creation from GMRT data
Clustering: Code for clustering single pulse events

CWITools: Tools for Cosmic Web Imager data
DarkBit: Dark matter constraints calculator
DarkCapPy: Dark Matter Capture and Annihilation
DDCalc: Dark matter direct detection phenomenology package
DeepShadows: Finding low-surface-brightness galaxies in survey images

DYNAMITE: DYnamics, Age and Metallicity Indicators Tracing Evolution
EvapMass: Minimum mass of planets predictor
frbcat: Fast Radio Burst CATalog querying package
GoFish: Molecular line detections in protoplanetary disks
GOTHIC : Double nuclei galaxy detector

GPCAL: Instrumental polarization calibration in VLBI data
HaloGen: Modular halo model code
HSTCosmicrays: Analyzing cosmic rays in HST calibration data
Kalkayotl: Inferring distances to stellar clusters from Gaia parallaxes
kīauhōkū: Stellar model grid interpolation

MCMCDiagnostics: Markov Chain Monte Carlo convergence diagnostics
PNICER: Extinction estimater
REBOUNDx: Adding effects in REBOUND N-body integrations
reproject: Python-based astronomical image reprojection
RRATtrap: Rotating Radio Transient identifier

Scintools: Pulsar scintillation data tools
SEDkit: Spectral energy distribution construction and analysis tools
TLC: Tidally Locked Coordinates
tlpipe: Data processing pipeline for the Tianlai experiment
wobble: Time-series spectra analyzer

October 2020 additions to the ASCL

Fifteen codes were added to the ASCL in October 2020:

Astronomaly: Flexible framework for anomaly detection in astronomy
Exo-DMC: Exoplanet Detection Map Calculator
grapus: GRavitational instability PopUlation Synthesis
GSpec: Gamma-ray Burst Monitor analyzer
LaSSI: Large-Scale Structure Information

Legolas: Large Eigensystem Generator for One-dimensional pLASmas
lenspyx: Curved-sky python lensed CMB maps simulation package
MBF: MOLSCAT 2020, BOUND, and FIELD for atomic and molecular collisions
Pix2Prof: Deep learning for textraction of useful sequential information from galaxy imagery
plancklens: Planck 2018 lensing pipeline

relxill: Reflection models of black hole accretion disks
ROGER: Automatic classification of galaxies using phase-space information
stella: Stellar flares identifier
stsynphot: synphot for HST and JWST
TACHE: TensoriAl Classification of Hydrodynamic Elements

Lightning talk at ADASS XXX: Making organizational software easier to find

The excellent ADASS XXX conference concluded yesterday. I missed meeting ADASS attendees face-to-face, but was delighted to spend time with them safely online, to learn about their projects and research, to talk about software and data, to share what the ASCL has been doing, and to meet old and new friends. The all-virtual conference was just about perfect; the technology set-up was excellent, providing opportunities to see sessions as they happened or at a later time on video, ask questions, comment on and discuss what was presented, and have one-on-one or small group video calls. The schedule was easy to keep track of, as one could subscribe to the schedule and get updates to it (mostly additions) immediately. Support was extremely responsive; an online Help Desk provided answers to queries almost immediately. There was even a conference photo!

Poster presenters were invited to record and upload a lightning talk — no more than three minutes — for their posters; two-minute lightning talks via Zoom were also arranged at the conference. The ASCL presented a poster on Making organizational software easier to find in ASCL and ADS; the hastily-put-together lightning talk presented at the conference for this poster is below.

ADASS attendee Simón Torres offered to download all the pre-recorded lightning talks and stream them during the conference, so a Poster Video Watching Party was scheduled for Wednesday afternoon. The stream was great fun to watch! It was interesting, too, to see all the different ways people presented their lightning talks.

What a great conference this was! I look forward to next year’s!

ADASS 2020 in the time of pandemic

Astronomical Data Analysis Software and Systems (ADASS), which was to have been in Granada, Spain this year, kicked off the fully online ADASS XXX meeting yesterday with four tutorials, as is usually done, though not quite like it was done this year. The Programming Organizing Committee and especially the Local Organizing Committee had to convert a conference that had been two years in the planning to a virtual meeting. This offered numerous challenges and learning opportunities! One challenge is that the conference is international; scheduling sessions for access to all participants couldn’t have been easy, but with the technology stack they chose, which includes the conference website, Zoom, YouTube, and Discord, and hard work, all of ADASS’s resources are available to all participants. One might have to get up early or stay up late to hear all of the talks live — the sleep-deprived author of this post awoke at 12:15 AM today to catch the opening sessions — but there are asynchronous options available, so groggy stumbling as one makes her way to the computer is a choice, not a requirement.

The ASCL has several presentations and activities this year. ASCL Chair Peter Teuben, ASCL Advisory Committee member Bruce Berriman, and I organized a Birds of a Feather (BoF) session on How to better describe software for discovery and citation today. We have organized BoFs focused on some aspect of software in the past, and, as in the past, this BoF offered a number of very short presentations and then open discussion.

The BoF session focused on software metadata, to improve how software is described and can be discovered and cited. After Teuben opened the session, Berriman presented his experience with using CiteAs to see how it suggested his software Montage be cited. CiteAs uses numerous ways to find a code’s citation method, including looking for metadata files — specific files that contain metadata for the software — on the code’s website and/or GitHub repository. Montage does not currently have a metadata file on its sites, so the citation method CiteAs suggested was not as robust as it could have been. The results of the search and its provenance are shown in the BoF’s slides, which can be downloaded at a link below.

This led nicely into my short talk on metadata files and how the ASCL can create a metadata file from an ASCL entry. The files the ASCL creates programmatically, codemeta.json and CITATION.cff, are intended to be starting points and contain placeholders for data the ASCL does not capture, but which we feel should be included in the metadata file; we encourage software authors to edit these files before they are placed on one’s code site.

Yan Grange, who had organized an earlier BoF on Best licensing practices, presented a summary of the session and the results of two of the several polls taken during that BoF.  Providing a license for your software is vitally important, as it lets others know what they can and cannot do with your software. Resources and other information from the earlier BoF are available online, and Grange’s summary slides for our software metadata BoF are included in the slides file below.

Teuben presented on several related topics: expanding or deepening a codemeta file with “API” information, the Unified Astronomy Thesaurus (UAT) and keywords, and the possibility of taking a software census at a niche science meeting. For this latter, he would like to take a well-defined field in astrophysics and have members of that community take an inventory of the software used and categorize it. He thinks a conference would be an ideal event for getting all the stakeholders together, and has identified a possible candidate conference for this activity.

The floor, if there can be a floor in a virtual meeting, was then open for comments, questions, answers and ideas, though discussion had already started in the Discord channel. One outcome of this session was that before the end of it, several participants had added metadata files to code repositories!

All slides for this session are in the PDF file below. If you would like more information about the session, please let us know in the comments section below, pinging us at ADASS if you are participating in the meeting, or by emailing me at

Slides (PDF)