v3.1.1

• Changes for compatibility with Pandas 1.3 (which broke convergence testing amongst other things).
• Updated docs with list of external likelihood codes, and to help avoid issues with PySide install
• Minor fixes in BAO/SN likelihoods

v3.1

Numerous changes for more general dependencies and parameterizations, mpi robustness and post-processing.
Fixes a bug in mcmc sampling with drag: True that gave incorrect results (but very small error when many dragging steps)

General

• updated and added documentation for cobaya-run-job; added cobaya-running-jobs and cobaya-delete-jobs
• Allow for more general dependencies between input parameters, derived parameters and likelihood/theory/prior inputs
• run, post and get_model can now all take inputs from a dictionary, yaml text or yaml
  filename
• Support resuming of a completed run with changed convergence parameters
• run has optional arguments to set debug, force, output, etc settings
• More input and output typing for easier static error detection; added cobaya.typing for static checking of input dictionaries using TypedDict when available
• Refactoring of cobaya.conventions to remove most string literals and rename non-private constants starting with _
• Uses GetDist 1.2.2+ which fixes sign loading the logposterior value from Cobaya
  collection
• Optimized calculation of Gaussian 1D priors
• run settings saved to ".updated.dill_pickle" pickle file in cases where callable/class
  content cannot be preserved in yaml (install "dill")
• File locks to avoid overwriting results accidentally from multiple non-MPI processes
• Commonly-used classes can now be loaded simply using "from cobaya import Likelihood, InputDict, Theory, ..." etc., or call e.g. cobaya.run(..)
• run and post return NamedTuples (same content as before)
• Fixed handling of "type" in external likelihood functions
• bib_script and doc_script can now be called programmatically
• MPI support refactored using decorators
• requirements can now also be specified as list of name, dictionary tuples (in case name needs to be repeated)
• renamed Collection -> SampleCollection (to avoid confusion with general typing.Collection)
• allow loading of CamelCase classes from module with lowercase name. Class "file_base_name" attribute to
  optionally specify the root name for yaml and bib files. Some supplied classes renamed.
• allow input likelihoods and theories to be instances (as well as classes); [provisional]

MCMC

• Fixed bug with "drag: True" that gave wrong results
• MPI reworked, now avoids ending and error deadlocks, and synchronizing exceptions
  (raising OtherProcessError on non-excepting processes)
• Random number generation now using numpy 1.17 generators and MPI seeds generated using SeedSequence
  (note MPI runs generally not reproducible with fixed seed due to thead timing/asynchronous mpi exchanges)
• Overhead reduced by at least 40%, thanks to caching in Collection
• Optimization of derived parameter output (for dragging, not computed at each dragging step)
• Some refactoring/simplification to pass LogPosterior instances more
• Reported acceptance rate is now only over last half chains (for MPI), or skipping first Rminus1_single_split fraction
• When no covamt or 'prosposal' setting for a parameter, the fallback proposal width is now scaled (narrower) from the ref or prior variance

Post-processing

• post function reworked to support MPI, thinning, and more general parameter-dependence
  operations
• On one process operating on list of samples outputs consistent list of samples rather
  than concatenating
• Output is produced incrementally, so terminated jobs still produce valid output
• No unnecessary theory recalculations
• Support for loading from CosmoMC/Getdist-format chains.
• Function in cobaya.cosmo_input.convert_cosmomc to general Cobaya-style info from
  existing CosmoMC chains (some likelihood/theory information may have to be added if you
  are recalculating things)

Minimize

• PyBOBYQA updated to 1.2, and quieter by default.
• 'best_of' parameter to probe different random starting positions (replacing seek_global_minimum for non-MPI)
• 'rhobeg' parameter larger to avoid odd hangs

Cosmology:

• Added CamSpec 2021 Planck high-l likelihoods (based on legacy maps, not NPIPE; thanks Erik Rosenberg)
• Added Riess et al H0 constraint (H0.riess2020Mb) in terms of magnitude rather than directly on H0
  (use combined with sn.pantheon with use_abs_mag: True; thanks Pablo Lemos)
• Install updated Planck clik code (3.1)

Tests

• Added MPI tests and markers, synchronize errors to avoid pytest hangs on mpi errors
• Added new fast but more realistic running, resuming and post tests with and without mpi
• Fixed some randomized test inputs for more reliable running
• drag: True running test
• Coverage reporting added to Travis
• More useful traceback and console log when error raised running pytest
• added COBAYA_DEBUG env variable that can be set to force debug output (e.g. set in travis for failed build rerun)