Category Archives: news

May 2022 additions to the ASCL

Twenty-five codes were added to the ASCL in May 2022:

am: Microwave through submillimeter-wave propagation tool for the terrestrial atmosphere
ASOHF: Adaptive Spherical Overdensity Halo Finder
ASTROMER: Building light curves embeddings using transfomers
BANG: BAyesian decomposiotioN of Galaxies
CPNest: Parallel nested sampling

CS-ROMER: Compressed Sensing ROtation MEasure Reconstruction
EarthScatterLikelihood: Event rates and likelihoods for Dark Matter direct detection in the presence of Earth-Scattering
FAlCon-DNS: Framework of time schemes for direct numerical simulation of annular convection
FHD: Fast Holographic Deconvolution
HOPS: Haystack Observatory Postprocessing System

hyperas: Keras + Hyperopt
Hyperopt: Distributed asynchronous hyper-parameter optimization
LATTE: Lightcurve Analysis Tool for Transiting Exoplanet
ld-exosim: Simulate biases using different limb darkening laws
LiSA: LIghtweight Source finding Algorithms for analysis of HI spectral data

maelstrom: Forward modeling of pulsating stars in binaries
MM-LSD: Multi-Mask Least-Squares Deconvolution
myRadex: Radex with a twist
PMOIRED: Parametric Modeling of Optical Interferometric Data
Pryngles: PlanetaRY spaNGLES

pyICs: Initial Conditions creator for isolated galaxy formation simulations
PyWPF: Waterfall Principal Component Analysis (PCA) Folding
QSOGEN: Model quasar SEDs
simulateSearch: High-time resolution data sets simulations for radio telescopes
Zelda: Generate correlation functions and power spectra from a galaxy catalog

ROSA2022: Reproducibility and Open Science in Astronomy workshop

This week, I’m attending and speaking at the ESO-sponsored Reproducibility and Open Science in Astronomy workshop. The first day was fabulous! The workshop runs through Thursday.

My talk is Opening the computational box: software sharing and the ASCL, and the abstract and links to resources mentioned in the talk are below.

Though computational methods are widely used in many disciplines, many researchers do not share the source code they develop, making their research difficult to verify and replicate. This presentation focuses on what software users and authors can do to share codes effectively, increase research reproducibility, and meet new requirements established by funders and journals. It will also cover how the Astrophysics Source Code Library (ASCL) improves the transparency of science by registering research code, its efforts to increase software findability, and how astronomers can get credit for their codes and better support the research record.

Slides (PDF)

Journals

Journal of Open Source Software (JORS)

Astronomy and Computing (A&C)

SoftwareX

Journal of Open Source Software (JOSS)

Computing and Software for Big Science

Research Notes of the AAS

Change leaders, guidelines, and tools

SciCodes/Nine Best Practices for Software Registries and Repositories

FORCE11/FORCE11 Software Citation Principles

Research Data Alliance/FAIR for Research Software (FAIR4RS) WG

CodeMeta/CodeMeta generator

CITATION file format (CFF)/CFF INIT

CiteAs

FAIR principles

Social coding sites and archival services

Bitbucket

GitLab

GitHub

Software Heritage

Figshare

Zenodo

Other resources and fun links

Asclepias

arXiv/arXiv Next Generation

DataCite

All ASCL entries in JSON

ASCL dashboard

Generating software metadata files from an ASCL entry:
codemeta.json example
CITATION.cff example

How many GitHub repos have CITATON.cff files/codemeta.json files?

April 2022 additions to the ASCL

Twenty codes were added to the ASCL in April 2022:

ADBSat: Aerodynamic Database for Satellites
Astroplotlib: Python scripts to handle astronomical images
Bayesian SZNet: Bayesian deep learning to predict redshift with uncertainty
DarkFlux: Dark Matter annihilation spectrum computer
dsigma: Galaxy-galaxy lensing Python package

FBCTrack: Fragmentation and bulk composition tracking
GADGET-4: Parallel cosmological N-body and SPH code
legacystamps: Retrieve DESI Legacy Imaging Surveys cutouts
MAYONNAISE: ADI data imaging processing pipeline
MonoTools: Planets of uncertain periods detector and modeler

ProFuse: Physical models of galaxies and their components
pySIDES: Simulated Infrared Dusty Extragalactic Sky in Python
RMNest: Bayesian approach to measuring Faraday rotation and conversion in radio signals
RSG: Redshift Search Graphs
RTS: Radio Transient Simulations

SCRIPT: Semi-numerical Code for ReIonization with PhoTon-conservation
SimAb: Planet formation model
SpECTRE: Multi-scale, multi-physics problem solver
TESS-Localize: Localize variable star signatures in TESS Photometry
TG: Turbulence Generator

March 2022 additions to the ASCL

Thirty-one codes were added to the ASCL in March 2022:

agnpy: Modeling jetted Active Galactic Nuclei radiative processes with Python
AutoSourceID-Light: Source localization in optical images
axionCAMB: Modification of the CAMB Boltzmann code
Bootsik: Potential field calculator

D2O: Distributed Data Object
easyFermi: Fermi-LAT data analyzer
exoVista: Planetary systems generator
fleck: Fast starspot rotational modulation light curves

GAMERA: Source modeling in gamma astronomy
imexam: IMage EXAMination and plotting
Magrathea-Pathfinder: 3D AMR ray-tracing in simulations
MAGRATHEA: Multi-processor Adaptive Grid Refinement Analysis for THEoretical Astrophysics

MAMPOSSt: Mass/orbit modeling of spherical systems
MaNGA-DAP: MaNGA Data Analysis Pipeline
MaNGA-DRP: MaNGA Data Reduction Pipeline
MG-MAMPOSSt: Test gravity with the mass profiles of galaxy clusters

MIRaGe: Multi Instrument Ramp Generator
NIMBLE: Non-parametrIc jeans Modeling with B-spLinEs
PetroFit: Petrosian properties calculator and galaxy light profiles fitter
pygacs: Toolkit to manipulate Gaia catalog tables

pyobs: Python framework for autonomous astronomical observatories
SATCHEL: Pipeline to search for long-period exoplanet signals
SetCoverPy: A heuristic solver for the set cover problem
SimLine: Radiative transfer in molecular lines

SISTER: Starshade Imaging Simulation Toolkit for Exoplanet Reconnaissance
starry_process: Interpretable Gaussian processes for stellar light curves
sympy2c: Generating fast C/C++ functions and ODE solvers from symbolic expressions
TAWAS: Wave equation solver

Vetting: Stand-alone tools for vetting transit signals in Kepler, K2 and TESS data
Wigglewave: Linearized governing equations solver
Zoobot: Deep learning galaxy morphology classifier

February 2022 additions to the ASCL

Twenty-six codes were added to the ASCL in February 2022:

ASPIRED: Automated SpectroPhotometric Image REDuction
Citlalicue: Create and manipulate stellar light curves
Contaminante: Identify blended targets in Kepler, TESS, and K2 data
distance-omnibus: Distance estimation method for molecular cloud clumps in the Milky Way

EDIV: Exoplanet Detection Identifier Vetter
EDIVU: Exoplanet Detection Identifier Vetter Unplugged
fiducial_flare: Spectra and lightcurves of a standardized far ultraviolet flare
Find_Orb: Orbit determination from observations

FIRE Studio: Movie making utilities for the FIRE simulations
GA Galaxy: Interacting galaxies model fitter
GALLUMI: GALaxy LUMInosity function pipeline
INSANE: INflationary potential Simulator and ANalysis Engine

NWelch: Spectral analysis of time series with nonuniform observing cadence
palettable: Color palettes for Python
popsynth: Observed surveys from latent population models
PSLS: PLATO Solar-like Light-curve Simulator

RFEP: Residual Feature Extraction Pipeline
SciCatalog: Tools for scientific data catalogs
Sculptor: Interactive modeling of astronomical spectra
SPARTAN: SPectroscopic And photometRic fiTting tool for Astronomical aNalysis

Starduster: Radiative transfer and deep learning multi-wavelength SED model
SunnyNet: Neural network framework for solving 3D NLTE radiative transfer in stellar atmospheres
SUPPNet: Neural network for stellar spectrum normalization
TERRA: Transit detection code

topoaccel: Topological acceleration scripts
Zwindstroom: Cosmological growth factors from fluid calculations

January 2022 additions to the ASCL

Fourteen codes were added to the ASCL in January 2022:

AllStarFit: R package for source detection, PSF and multi-component galaxy fitting
AltaiPony: Flare finder for Kepler, K2, and TESS light curves
AstroToolBox: Java tools for identifying and classifying astronomical objects
BLOSMapping: Determine line-of-sight magnetic fields of molecular clouds
COWS: Cosmic web filament finder

dark-photons-perturbations: Dark photon conversions in our inhomogeneous Universe
disnht: Absorption spectrum solver
EzTao: Easier CARMA Modeling
fermi-gce-flows: Infer the Galactic Center gamma-ray excess
FitsMap: Interactive astronomical image and catalog data visualizer

MAGRATHEA: Planet interior structure code
nProFit: n-Profile Fitting Tool
statmorph: Non-parametric morphological diagnostics of galaxy images
tellrv: Radial velocities for low-resolution NIR spectra

December 2021 additions to the ASCL

Twenty-seven codes were added to the ASCL in December 2021:

AsteroGaP: Asteroid Gaussian Processes
BayesicFitting: Model fitting and Bayesian evidence calculation package
DarkARC: Dark Matter-induced Atomic Response Code
deeplenstronomy: Pipeline for versatile strong lens sample simulations
Defringe: Fringe artifact correction

DiracVsMajorana: Statistical discrimination of sub-GeV Majorana and Dirac dark matter
FTP: Fast Template Periodogram
GRIT: Gravitational Rigid-body InTegrators for simulating coupled dynamics
hankl: Python implementation of the FFTLog algorithm for cosmology
HoloSim-ML: Analyzing radio holography measurements of complex optical systems

Interferopy: Analyzing datacubes from radio-to-submm observations
JexoSim 2.0: JWST Exoplanet Observation Simulator
l1p: Python implementation of the l1 periodogram
MISTTBORN: MCMC Interface for Synthesis of Transits, Tomography, Binaries, and Others of a Relevant Nature
NeutrinoFog: Neutrino fog and floor for direct dark matter searches

O’TRAIN: Optical TRAnsient Identification NEtwork
Optab: Ideal-gas opacity tables generator
pycelp: Python package for Coronal Emission Line Polarization
QUESTFIT: Fitter for mid-infrared galaxy spectra
Qwind: Non-hydrodynamical model for AGN line-drive winds

Qwind3: Modeling UV line-driven winds originating from accretion discs
SAPHIRES: Stellar Analysis in Python for HIgh REsolution Spectroscopy
SCORPIO: Sky COllector of galaxy Pairs and Image Output
STDPipe: Simple Transient Detection Pipeline
TESSreduce: Transient focused reduction for TESS data

WIMpy_NREFT: Dark Matter direct detection rates detector
wpca: Weighted Principal Component Analysis in Python

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

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

September 2021 additions to the ASCL

Thirty codes were added to the ASCL in September:

alpconv: Calculating alp-photon conversion
BHJet: Semi-analytical black hole jet model
BiPoS1: Dynamical processing of the initial binary star population
DviSukta: Spherically Averaged Bispectrum calculator
eMCP: e-MERLIN CASA pipeline

Frankenstein: Flux reconstructor
gammaALPs: Conversion probability between photons and axions/axionlike particles
GLoBES: General Long Baseline Experiment Simulator
gphist: Cosmological expansion history inference using Gaussian processes
Healpix.jl: Julia-only port of the HEALPix library

HSS: The Hough Stream Spotter
HTOF: Astrometric solutions for Hipparcos and Gaia intermediate data
Menura: Multi-GPU numerical model for space plasma simulation
OSPREI: Sun-to-Earth (or satellite) CME simulator
pyFFTW: python wrapper around FFTW

pyia: Python package for working with Gaia data
Rubble: Simulating dust size distributions in protoplanetary disks
ShapeMeasurementFisherFormalism: Fisher Formalism for Weak Lensing
SkyCalc_ipy: SkyCalc wrapper for interactive Python
SkyPy: Simulating the astrophysical sky

SNEWPY: Supernova Neutrino Early Warning Models for Python
Snowball: Generalizable atmospheric mass loss calculator
SNOwGLoBES: SuperNova Observatories with GLoBES
SoFiA 2: An automated, parallel HI source finding pipeline
STAR-MELT: STellar AccrRtion Mapping with Emission Line Tomography

unpopular: Using CPM detrending to obtain TESS light curves
Varstar Detect: Variable star detection in TESS data
VOLKS2: VLBI Observation for transient Localization Keen Searcher
WeakLensingDeblending: Weak lensing fast simulations and analysis of blended objects
WimPyDD: WIMP direct–detection rates predictor