Release 1.2 - 2023-09-18

Documentation

• Various minor improvements of documentation
• Update documentation layout
• Clean up documentation of Python classes and functions in infrared namespace
• Improve application example notebook
• Add applications examples: graph coloring, automata and network parsimony
• Elaborate documentation of def_constraint_class, def_function_class

Python library

• New defaults and additional parameters for targeted sampling (multi-dimensional Boltzmann sampling)
• Add error checking in def_constraint_class, def_function_class

C++ library

• Rename class ired:ConstraintNetwork to ired:FeatureNetwork

Release 1.1 - 2022-11-15

This release improves support for stochastic optimization based on resampling (among some minor improvements and adapations)

C++ library

• Introduce support for resampling by restricted traceback. The functionality is directly supported by the Infrared engine without need for recomputation of the partition function.

Python interface

• Resampling functionality is provided by methods resample() of ir.Sampler and ir.PFClusterTree
• Add ir.mc_optimize for optimization

Documentation

• Update the bookchapter tutorial - use new resampling mechanism

Release 1.0 - 2022-11-15

This release facilitates the modeling of sampling and optimization problems from a much broader range of applications by

• introducing a new modeling syntax which facilitates the definition of constraint models and supporting the definition of new constraints and functions with simple Syntax in Python
• enabling modeling in a truly declarative and compositional style
• supporting domain bounds, which can be performance critical for many applications
• optimizing space requirements
• enabling optimization in addition to sampling, where both can be based on the same constraint model
• improving the API documentation
• adding tutorials and examples in Jupyter notebooks that demonstrate the modeling of design problems in the framework

Python interface

• Introduce new modeling syntax to define constraint network models based on a new class Model
• Old class ConstraintNetwork is merged with new class Model
• Support targeting of only selected features
• Revise syntax for the definition of function and constraints
• Add support for optimization (in addition to sampling)
  • allow to select evaluation algebra
  • introduce weighted functions
• Support IUPAC sequence constraints with a specific form of constraint simplification
• Rename functions and constraints in module rna
• Support named variables in constraint models

C++ library

• Support upper and lower bound of variable domains; add class FiniteDomain
• Remove dependency on boost::graph
• Implement traceback for constraint optimization
• Optimize space consumption of materialized functions and constraints by using a specialized replacement SimpleMap of standard sparse containers like std::hash_map
• Add evaluation in arctic semiring for constraint optimization

Documentation

• Revisit API documentation
• Adapt tutorial notebook to new Python interface
• Add example for multi target design from Python code (Jupyter notebook)
• Add Jupyter notebook as supplement of a book chapter on Infrared with new example code
• Add tags to sync with book chapter

Build system

• Update setup.py

Bug fixes

• Fix bug of repeated dependencies in the specification of models
• Fix undefined behavior in the materialization of functions/constraints

Release 0.5.1 - 2021-07-10

Python Interface

• Export algebra for constraint optimization
• Redefine constraints and functions in Python

C++ library

Materialization of functions /and/ constraints

• supports the definition of functions and constraints in Python without performance penalties
• the existing mechanism for functions was extended to constraints

Bug Fix

• Update behavior of BoltzmannSampler.plot_td()

Documentation

• Re-enable API documentation via doxygen
• Update tutorial jupyter notebook

Release 0.5 - 2021-05-04

C++ library

Use pybind11

Installation and dependencies

• Change build mechanism to setup.py and cmake
• Enable installation via pip and conda

Release 0.4 - 2020-11-08

Python Interface

• Refactor and streamline the Python interface
• Support tree decomposition by networkx, improve the tree decomposition interface
• Add access to partition function and provide consistency check in

Documentation

• Add tutorial of the Python interface (Jupyter notebook)

C++ library

• Add tests, fix handling of inconsistent networks
• Revert to using boost::python (to resolve a bug in the use of pybind11)

Installation and dependencies

• Improve installation via autotools
• Replace dependency on libhtd by networkx

Release 0.3 - 2018-08-17

• Generalize Python classes for Boltzmann sampler construction and provide them in Python module infrared for simpler use of the lib
• Implement multi-dimensional Boltzmann sampling and provide this functionality via module infrared

Release 0.2.1 - 2018-08-08

• Add/cleanup Doxygen documentation of Python modules

Release 0.2 - 2018-08-07

• Improve program comments, support doxygen (make doxygen-doc)
• Revise code, fix make check

Release 0.1 - 2018-08-07

• Optimize infrared evaluation/sampling engine
• Optimize tree decomposition using libhtd
• Cleanup treedecomp and redprint Python code and add features
• Bugfixes
• Implement some tests

Release 0.0.1 - 2018-08-02

Initial release