I’ve posted before about where the codes are; here’s a pie that shows the relative use of Github, Google Code, Bitbucket, and Sourceforge. Please note that because all the Starlink codes are in one Github repo, that repo is represented only once in the pie below. Want to do your own analysis? The site links (1080 of them at the moment, as some codes have more than one) are available here.
Fourteen codes were added to the ASCL in December 2014:
BRUCE/KYLIE: Pulsating star spectra synthesizer
Cheetah: Starspot modeling code
CRPropa: Numerical tool for the propagation of UHE cosmic rays, gamma-rays and neutrinos
DAMIT: Database of Asteroid Models from Inversion Techniques
GeoTOA: Geocentric TOA tools
HMF: Halo Mass Function calculator
Hrothgar: MCMC model fitting toolkit
MMAS: Make Me A Star
PIAO: Python spherIcAl Overdensity code
SoFiA: Source Finding Application
SOPHIA: Simulations Of Photo Hadronic Interactions in Astrophysics
TraP: Transients discovery pipeline for image-plane surveys
URCHIN: Reverse ray tracer
UTM: Universal Transit Modeller
This is an update on figures I’ve previously shared (most recently here). Currently, the ASCL indexes 977 codes. The percentage of these codes housed on social coding sites are:
GitHub: 8.1%
SourceForge: 4.2%
Code.Google: 2.8%
Bitbucket: 1.3%
This gives us 16.4% of codes listed on the ASCL housed on a public social coding site, an increase since February of 5.4%, most of this from GitHub (up from 4.2% in February), though the percentages of four sites have increased.
As I said in February, I expect the percentage of codes on social coding sites will continue to grow, especially since GitHub’s use is increasing quickly in the community. One factor some credit for this increase is that GitHub has made it easy to push code to Zenodo for archiving and DOI minting, and providing another way to cite code.*
As mentioned in my previous post, how codes are cited vary. Software citation will be the main topic at Tuesday’s inaugural Software Publishing Special Interest Group meeting at AAS225, which will be held at 3:45 PM in 615 of the Convention Center. If you are at AAS this week, you are welcome to attend and I hope to see you there!
*It was reported at .Astronomy6 that “some astro journals won’t even accept a DOI as a citation.” I don’t know which journals and hope someone will enlighten me; I would like to know the rationale for that stance and would gladly take this up with publishers.
One of the unconference sessions (proposed during the event) held at December’s .Astronomy was on software citation, this subject having come up in an earlier session on improving credit for software.
Discussion and comments in the session inspired me to look at astronomy’s current practices for citing software. Though not an exhaustive list, I looked in more than a dozen journals for citations for codes used in research, and below are some of the examples I gathered.
The most common way to cite software is to reference a paper describing the code. This is how, for example, the authors of yt would like that software cited, as shown from a recent MNRAS paper:
Sometimes a link to the website for a code is listed as a reference to it, as was done in a Classical and Quantum Gravity paper:
Conference proceedings are cited in some cases, as the citation below for WCSTools in an The Astrophysical Journal paper demonstrates:
ASCL entries can be cited, too, as shown in this citation for pynbody in a paper published in Physical Review D:
Someone — I don’t remember who — reported that Google Scholar does not index mentions of codes, GitHub repos, etc. as citations, because they are not papers. An opinion tweeted out about this summed up the sentiment in the room pretty well! I plan to take this up with Google after the AAS meeting. Fortunately, ADS does index properly formatted software references; the only reference listed in this post that I didn’t see captured by ADS was the URL for CAMB, which is not surprising (nor expected).
A subsequent post will include additional information and a list of resources about software citation, to be posted before the first Special Interest Group on software publishing meeting scheduled at AAS225 that will be held on Tuesday, January 6, from 3:45 PM – 4:45 PM in 615 in the Convention Center. The main topic of this meeting will be software citation, and all interested parties are welcome to attend.
The journals below were part of my hunting grounds for software citations. Ever had a citation to software you used in research refused by a publication? If so, I’m interested in knowing the details; please share here or send them to editor@ascl.net. Thanks!
American Institute of Physics Proceedings
Astronomy & Astrophysics
Astronomy and Computing
The Astronomical Journal
The Astrophysical Journal
The Astrophysical Journal Supplement
Classical and Quantum Gravity
Icarus
Monthly Notices of the Royal Astronomical Society
Nature
Physical Review D
Proceedings of the SPIE
Publications of the Astronomical Society of Australia
Publications of the Astronomical Society of Japan
Publications of the Astronomical Society of the Pacific
Additional screenshots of software citations:
Formatting counts! Below, two citations for Turbospectrum, the first formatted in a way ADS can pick up and count the citation, the second one not.
The ASCL is at .Astronomy (“dot astronomy”), which officially starts tomorrow morning. Three days of unconference, discussion, sessions, hacking, ideas, collaborating, fun, cool buttons, and, rumor has it, Belgian chocolate, in the magnificent city of Chicago. Follow along on Twitter, hashtag #dotastro!
Twenty-seven codes were added in November:
Anmap: Image and data analysis
BKGE: Fermi-LAT Background Estimator
CGS3DR: UKIRT CGS3 data reduction software
ECCSAMPLES: Bayesian Priors for Orbital Eccentricity
Flicker: Mean stellar densities from flicker
galpy: Galactic dynamics package
GPI Pipeline: Gemini Planet Imager Data Pipeline
HOPE: Just-in-time Python compiler for astrophysical computations
iDealCam: Interactive Data Reduction and Analysis for CanariCam
JCMT COADD: UKT14 continuum and photometry data reduction
NAFE: Noise Adaptive Fuzzy Equalization
NDF: Extensible N-dimensional Data Format Library
NEAT: Nebular Empirical Analysis Tool
OPERA: Open-source Pipeline for Espadons Reduction and Analysis
POSTMORTEM: Visibility data reduction and map making package
pyGadgetReader: GADGET snapshot reader for python
PyMGC3: Finding stellar streams in the Galactic Halo using a family of Great Circle Cell counts methods
pysovo: A library for implementing alerts triggered by VOEvents
Raga: Monte Carlo simulations of gravitational dynamics of non-spherical stellar systems
RC3 mosaicking pipeline: Creating mosaics for the RC3 Catalogue
segueSelect: SDSS/SEGUE selection function modelling
sic: Sparse Inpainting Code
SPOTROD: Semi-analytic model for transits of spotted stars
SPT Lensing Likelihood: South Pole Telescope CMB lensing likelihood code
Starlink Figaro: Starlink version of the Figaro data reduction software package
util_2comp: Planck-based two-component dust model utilities
voevent-parse: Parse, manipulate, and generate VOEvent XML packets
Five codes were added to the ASCL in October:
DIAMONDS: high-DImensional And multi-MOdal NesteD Sampling
GIZMO: Multi-method magneto-hydrodynamics+gravity code
MEPSA: Multiple Excess Peak Search Algorithm
RICH: Numerical simulation of compressible hydrodynamics on a moving Voronoi mesh
UVOTPY: Swift UVOT grism data reduction
Thirteen codes were added to the ASCL in September:
CHLOE: A tool for automatic detection of peculiar galaxies
CosmoSIS: Cosmological parameter estimation
IM3SHAPE: Maximum likelihood galaxy shear measurement code for cosmic gravitational lensing
IFSFIT: Spectral Fitting for Integral Field Spectrographs
IFSRED: Data Reduction for Integral Field Spectrographs
iSpec: Stellar atmospheric parameters and chemical abundances
LANL*: Radiation belt drift shell modeling
mixT: single-temperature fit for a multi-component thermal plasma
Nahoon: Time-dependent gas-phase chemical model
ORBS: A reduction software for SITELLE and SpiOMM data
rmfit: Forward-folding spectral analysis software
Slim: Numerical data compression for scientific data sets
Tsyganenko Geomagnetic Field Models