Code Repositories¶

Statistics¶

• pymultinest-tutorial: pymultinest tutorial

• PyMultiNest: Pythonic Bayesian inference and visualization for the MultiNest Nested Sampling Algorithm or MCMC.

• RMultiNest: R wrapper for MultiNest

• APEMoST: Automated Parameter Estimation and Model Selection Toolkit – A fast MCMC implementation for Bayesian inference

• syscorr: Bayesian correlation swiss army knife

• MultiNest: MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.

• PyDNest: Python connection to Diffusive Nested Sampling.

• stagedstan: Staged Stan Python package

• cuba: Cuba - a library for multidimensional numerical integration

• jbopt: Parameter space exploration toolbox

• Bookmarks:

  • –> superpy: Scan the CMSSM with (py)MultiNest and plot the results with a new plotting GUI.
  • –> MultiNest: MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.

Scientific data analysis¶

• nfftpy: Python interface to NFFT library

• nfft: Fast Fourier transform at nonequispaced nodes

• regulargrid: Regular Grid Multivariate linear interpolation

• pyblocxs: Bayesian Low-Count X-ray Spectral (BLoCXS) analysis in the Sherpa environment

• BXA: Bayesian X-ray analysis (nested sampling for Xspec and Sherpa)

• libnova: libnova is a general purpose, double precision, Celestial Mechanics, Astrometry and Astrodynamics library.

• mcl: MCL - a cluster algorithm for graphs (from http://micans.org/mcl/)

• uncertainties: Transparent calculations with uncertainties on the quantities involved (aka “error propagation”) ; calculation of derivatives. [Python package]

• Bookmarks:

  • –> pyblocxs: Bayesian Low-Count X-ray Spectral (BLoCXS) analysis in the Sherpa environment
  • –> pyblocxs: Bayesian Low-Count X-ray Spectral (BLoCXS) analysis in the Sherpa environment
  • –> pyblocxs: Bayesian Low-Count X-ray Spectral (BLoCXS) analysis in the Sherpa environment

Presentation¶

• multitalk: Fork of multitalk, a nonlinear presentation software

• Bookmarks:

  • –> reveal.js: The HTML Presentation Framework

Productivity¶

• redshift: Redshift adjusts the color temperature of your screen according to your surroundings. This may help your eyes hurt less if you are working in front of the screen at night.

• note3: Notational Velocity clone written with Jython+SWT

• spuren: A Desktop search engine kept fast and simple

• workflow-copilot: Profile your computer interaction and interrupt with news only when appropriate

• Bookmarks:

  • –> redshift: Redshift adjusts the color temperature of your screen according to your surroundings. This may help your eyes hurt less if you are working in front of the screen at night.

Scientific Documentation¶

• LocalCopy: LocalCopy is a plugin that extends the popular reference manager JabRef. It provides an automatic download feature for preprints from the arXiv and journals that are linked using the DOI-system or that specify an URL link.
• Bookmarks:

Data visualization¶

• matplotlib-subsets: Hierarchical subset diagram plotting for Python/Matplotlib

• webscipy: Interactive web pages for scientific computing with python

• matplotlib-xkcdify: sketchy, imprecise plotting theme for matplotlib

• Bookmarks:

  • –> bokeh: Interactive Web Plotting for Python
  • –> matplotlib-venn: Area-weighted venn-diagrams for Python/matplotlib

Scheduling¶

• ska-SchedEng-demo-nrao-field-system: SchedulingEngine interface for controlling NRAO field system
• ska-SchedUI: Scheduling Web Interface for large telescope arrays
• ska-SchedEng: Scheduling Engine for large telescope arrays
• Bookmarks:

Distributed Computing¶

• Jarsync: Java implementation of the Rsync protocol based on Jarsync by Casey Marshall

• ics: The Interclient Communication Service provides low-level clients communication methods

• fss: A computer-independent view and addressing scheme of a common folder.

• Jake: Collaborating on a project for ordinary people

• udt-java: Java implementation of UDT (based on http://udt-java.sf.net by Bernd Schuller’s)

• availablelater: AvailableLaterObjects simplify writing asynchronous calls by decoupling the result and hiding Thread creation.

• externals: Converting Java projects to Maven without breaking Upstream

• Bookmarks:

  • –> jstun2: Java STUN2 (RFC5389) implementation, based on JSTUN by Thomas King
  • –> astropysics: Astrophysics utilities for python
  • –> scam: Create publication quality 3D graphics using GNU Guile and cairo.
  • –> Jake: Collaborating on a project for ordinary people

File systems¶

• fusepy: Simple ctypes bindings for FUSE

• chunk-fuse: Filesystem in User Space (fuse) using compressed and encrypted chunks

• fresh-torrents: Helps you find popular, cheap (bandwidth-wise) and new torrents

• archivemount: FUSE filesystem using libarchive

• sparse-reiserfs-manager: Script to create and resize reiserfs sub-filesystems stored in sparse files.

• Bookmarks:

  • –> reiserfs-defrag: Offline defragmentation utility for reiserfs (v3.6)
  • –> fusepy: Simple ctypes bindings for FUSE

Networks¶

• digestaps: Digest Authorization Proxy Server
• DHCProbe: Send a DHCP request to DHCP server to check its configuration
• Bookmarks:

Other¶

• DNest3: Diffusive Nested Sampling

• python-epub-builder: Python API for building EPUB books

• nifty: NIFTY - Numerical Information Field Theory

• nested-sampling: **

• research2epub: Linearize research papers into readable ebooks.

• hamiltonian-nested-sampling: Nested Sampling with Constrained Hamiltonian Monte Carlo (by Michael Betancourt)

• progressbar: An easy-to-use C library for displaying text progress bars.

• imagehash: A Python Perceptual Image Hashing Module

• verynice: A Dynamic Process Re-nicer

• sci: Gentoo Science Overlay

• PyMirage: Automatically generate playlists of similar music

• k2pdfopt: K2pdfopt re-flows text from multi-column PDF/DJVU files for e-readers and smartphones

• Bookmarks:

  • –> pypmc: **
  • –> RNested: Nested Sampling algorithm implemented in R
  • –> python-sty: Embed Python in LaTeX
  • –> maven-python-mojos: A collection of Maven plugins to help integrate Python tools into Java shops
  • –> ggplot: ggplot for python
  • –> impress.js: It’s a presentation framework based on the power of CSS3 transforms and transitions in modern browsers and inspired by the idea behind prezi.com.
  • –> VortonSim: CPU-based Vorton Simulation
  • –> pyautodiff: Automatic differentiation for NumPy
  • –> pystan: PyStan: Python interface to Stan
  • –> pyautodiff: Automatic differentiation for NumPy

Parameter optimization¶

• condor_optimization: CONDOR (COnstrained, Non-linear, Direct, parallel Optimization using trust Region method for high-computing load function) allows continuous parameter optimization
• Bookmarks:

Code Snippets (Gists)¶

• install.rst: Prepare VirtualBox image
• howlong.py: ETA from external programs
• updateGentoo.sh: update Gentoo Linux
• runProcess.py: launch process
• thunderbird_build_notes.txt: Thunderbird/Mozilla build notes
• publishPython.sh: tool for publishing sphinx documentation on github and releasing packages on PyPI
• installMultiNest.sh: install {,Py,R}MultiNest
• caching.py: joblib caching for expensive functions
• pbar.py: Python progressbar