Changes

Development version

The development version contains changes that have not yet been tested well enough to be added to the main version. It has more features than numbered versions but you should also expect more bugs. See the development page for more details.

Version 1.4

Version 1.3

Sampling

Fisher matrix sampler
New GaussianLikelihood superclass to help add Fisher-compatible Gaussian likelihoods

##Standard Library Additions

Planck 2015 Likelihood
The Dark Energy Survey Science Verification Weak Lensing 2-point likelihood, including:
- Photometric redshift bias marginalization
- Shear bias marginalization
- Power law intrinsic aligment models
- xi(theta) likelihood
Add a utility to delete data block sections for more complex pipelines
Add matter and galaxy 2D C_ell spectra, and magnification, as well as their cross-correlations

##Standard Library Updates

Allow extrapolate_power to work downwards to kmin as well as kmax
Allow switching off distance output in FrankenEmu
Modify several likelihoods to support Fisher matrices
Fix linking on OSX Yosemite

##Standard Library Bug Fixes

Fix Planck Makefiles to work in Ubuntu - thanks to Matteo Costanzi
Fixed the "root" option
Improvement to customizability of various modules
Fix CAMB slowdown when P(k) not needed by exposing kmax parameter
Change how LAPACK is linked to enable easier custom linking
Fix a bug where the wrong values was used in BBN
Fix a compile error in the fgas module under newer gcc versions

Core Features

Lock output files when they are created to raise an error whey you accidentally leave out the --mpi flag or run two jobs with the same output file name.
Added a collection of physical constant values for use in modules (list taken from astropy.constants). In python: "import cosmosis.constants". In C: "#include cosmosis_constants.h". In Fortran: "#include cosmosis_constants.fh".
Save priors in the head of the output file
Allow the grid sampler to save its outputs progressively
Warn if more than 1 million grid points requested in the grid sampler
Enable saving chains in FITS format as well as text format

Postprocessing

Enable adding extra derived parameters during postprocessing with user-defined functions
Add weighted MCMC scatter plots
Added lower and upper 95% limit statistics
Enable postprocessing importance samples
Enable plotting multiple different sampler outputs in one plot
Enable plotting only some of the chain parameters
Select whether you want transparent or opaque contours
Add scatter plot for weighted MCMC
Fix unusual factor of 100 appearing in some scatter plots
Add options to postprocess only a subset of 2D plots to save time
Fix a crash when plotting only one likelihood in P(k) test sampler plots (thanks to Tom McClintock)
Enable postprocessing FITS chains
Fix a bug when postprocessing PMC chains

Core Bug Fixes

Fix burning a fraction of the chain rather than a fixed number of samples when postprocessing
Fix a crash when one column was an exact linear function of another
Fix a bug that gave wrong MCMC median values

Version 1.2

###Samplers

Added Population Monte Carlo sampler
Added Snake grid sampler
Added Kombine ensemble sampler
Added List simple sampler
(Experimental) Enable making a graphical representation of a pipeline in the test sampler
Improved documentation pages of all the samplers

###Postprocessing

Add blinding option to post-processing
Enable postprocessing directory of cosmology results
Allow postprocessing MCMCs with weight columns
Fix which columns are plotted in post-processing
Add flag to swap x and y axes in plots

###Standard Library Updates

Added MGCAMB
Added FrankenEmu Cosmic Emulator
Added Nicaea code for lensing C_ell -> xi(theta)
Added Lucy Clerkin bias code
Added Wrapper for CLASS Boltzmann code
Added Cluster f_gas likelihood by Adam Mantz
Added BBN YHe consistency module by Adam Mantz
Added Balmes-Corasaniti strong lensing likelihood
Added Suyu strong lensing likelihood
Added WiggleZ BAO likelihood
Updated to new version of isItGR
Added CAMB Jan 2015
Added a new format mode des_fmt to photo-z loader
Enable multiple renames in rename module
Enable using different consistency relation file in consistency module

###Standard Library Bugs

Fixed linear alignment code
Fixed bug with covariance being wrong for CFHTLenS
Fixed error when z_min>0 in photo-z distributions
Fixed some compilation problems with Planck likelihood v1
Fix nan errors when A=0 in intrinsic alignments

###Installation

Installer now works on Yosemite
Installer should be easier to update in future

###Infrastructure

Improve datablock logging facilities
Fix bugs with priors not working properly
Improved repository creation tool
Added an error reporting tool
Added a tool to download an existing module from a git/hg url
Added a tool to check for uncommitted changes

##Version 1.1

There are two changes in v1.1 is that might break your runs:

you now should specify --mpi when running multinest in MPI mode
you may need to change some double parameters (like some of the planck nuisance params) from integers by adding .0 on the end

Standard library

Include small heliocentric correction to JLA supernova likelihood
Add isItGR modified gravity camb
Add newer Takahashi Halofit
Add module to log-linearly extrapolate matter power spectra
Add intrinsic aligments to weak lensing shear spectra
Add Linear Alignment model for intrinsic weak lensing alignments in several variants (Bridle & King, Bridle & King Corrected, and Kirk, Rassat, Host & Bridle)
Fix bugs stopping BBN likelihood from working at all
Add a PPF shear spectra calculation
Add utility functions to Limber approximation library
Increase accuracy of C_ell -> xi(theta) code
Add module that lets you sample in sigma_8 by re-scaling the output from CAMB.
Add mass functions from the CRL with numerical recipes replaced

Samplers

Fix multinest MPI output problem where part of file overwritten
Enable saving data outputs in grid sampler
Fix bug saving additional output like sigma_8 from multinest
Let test sampler save as tgz output

Demos

Add new demos and split off longer demos into "examples" directory
Tweak amount of output in demo 6.
Use PLANCK_DATA_DIR environment variables in Planck demos
Demo 10: Smith Halofit versus Takahashi Halofit (plotting multiple ini files)
Demo 11: Modified gravity effect on shear spectra (grid sampling saved as tgz)
Demo 12: Extreme value stats for cluster masses
Example A: Old demo 10, moved.
Example B: Sample CFHTLenS with intrinsic aligments and sigma_8 (compare two models)
Example C: Multinest Planck (saving to sql?)

Infrastructure

Allow environment variables in ini files
Update self-updater code to be able to checkout development version
Enable saving multiple 2D grids in Fortran
Enable saving datablocks to single tgz files
Fix saving/loading metadata after finishing the chain in text output files
Enable using environment variables in ini files
Enable integer parameters in values files being passed to pipelines

Post-processing

Fix plotting grid samples in cases with a very large range in likelihoods
Fix bug in Dunkley power spectrum testing printing repeated values
Stop grid plots from including 2D plots of likelihood versus parameter
Output all citations required by the pipeline

Version 1.0

Version 1.0 is the first fully released version of cosmosis.

If you have a module for a pre-release version then you may need to make minor changes to it. The main is that you may need to change how python modules import cosmosis features:

#!python
#Old:
from cosmosis import names, option_section
#New:
from cosmosis.datablock import names, option_section

If you have developed module for the prototype des-pipe code then the interface functions have been changed significantly. See the documentation linked from the modules page for more information.

Wiki

cosmosis / changelog-temp