v2.6.4

Programs

• Fix C++17 compilation issue with kinwalker
• Fix potential compilation issues with C++20 in RNAforester frontend
• Refactor and correct spelling issues in man pages for several executable programs

Library

• API: Add shift move support to vrna_move_neighbor_diff*() functions
• API: Fix char array initialization in snoop.c
• API: Fix potentially leaking file pointer in vrna_file_msa_read()
• API: Fix potentially leaking memory in rnaplot_EPS()
• API: Fix potential use of uninitialized variable in vrna_rotational_symmetry_db_pos()
• API: Fix soft constraints issue in external loop of vrna_subopt*()
• SWIG: Add swig class output parameter typemap for Python
• SWIG: Add __hash__() and __eq__() methods for wrapped _vrna_move_t in Python
• SWIG: Return var_array<vrna_move_t> objects in Python wrapped vrna_neighbors() and vrna_move_neighbor_diff()
• SWIG: Refactor file handle wrapping between Python 3 and C
• SWIG: Fix var_array Python slices and associated memory leak
• SWIG: Fix bogus delete/free() calls in swig interface
• Add requirements to build RNAlib with MSVC for Windows
• Remove unused code in RNApuzzler

Package

• DOC: Transition reference manual from doxygen to sphinx via breathe bridge
• DOC: Merge documentation of C-API and Python API
• DOC: Merge parts of tutorial into reference manual
• AUTOCONF: Refactor autoconf checks for capability to build reference manual
• AUTOCONF: Deactivate build of RNAxplorer if lapack requirements are not met

v2.6.3

Library

• Make JSON parser integral part of ViennaRNA library
• API: Move modified energy parameters into 'modified_base' object in JSON file(s)
• SWIG: Enable stand-alone build of Python interface (for PyPI)

Package

• Add enthalpy and terminal end values for predicted stacks with dihydrouridine
• TESTS: Allow for using pytest to test the Python 3 interface

v2.6.2

Programs

• Fix preparation of input sequences for modified base support in RNAcofold

Library

• Fix energy corrections for modified base support when unmodified base is not the same as fallback base, e.g. in the case of inosine
• Add soft constraints to multifold external loop decomposition
• Add soft constraints preparation stage callback
• SWIG: Fix fc.sc_add_bp() propagation of constraint values
• SWIG: Wrap energy parameter file strings

Package

• TESTS: Add modified base tests on duplex data with I-C and A-Psi pairs from publications

v2.6.1

Programs

• Fix double free corruption in RNAdos
• Fix compilation issues due to use of uint instead of unsigned int for RNAxplorer
• Fix compilation issues for RNAxplorer when OpenMP is unavailable

Package

• AUTOCONF: Update autoconf macros
• Update Debian-based packaging rules

v2.6.0

Programs

• Add modified base input support to RNAfold
• Add modified base input support to RNAplfold
• Add modified base input support to RNALfold
• Add modified base input support to RNAcofold
• Add modified base input support to RNAsubopt
• Fix missing strand separators in RNAsubopt when applied to multiple interacting sequences
• Fix sorted output in RNAsubopt with --gquad option
• Allow for only -Fp in RNAinverse instead of always activating -Fm
• Fix default value of RNAinverse -R option in manpage
• Restructure --*help output and man pages for most executable programs
• Allow for cation concentration (Na+) changes in most executable programs (default 1.021M)
• Allow for at least as many threads as CPUs are configured if maximum thread number detection fails
• Fix alignment input parsing in refold.pl
• Add RNAxplorer program to the distribution

Library

• API: Extend model_details to allow for salt concentration changes
• API: Add functions for salt concentration change derived energy corrections in ViennaRNA/params/salt.h
• API: Add arbitrary modified base support (vrna_sc_mod()) via soft constraints mechanism and JSON input data
• API: Add Pseuoduridine-A parameters via soft constraints callback
• API: Add Dihydrouridine parameters via soft constraints callback
• API: Add inosine-U and inosine-C parameters via soft constraints callback
• API: Add m6A parameters via soft constraints callback mechanism
• API: Add 7DA modification support via soft constraints
• API: Add Purine (nebularine) modification support
• API: Add new soft constraints multi-callback dispatcher
• API: Add dynamic array data structure utilities
• API: Add string data structure utilities
• API: Add vrna_strchr() function
• API: Fix potential problems in free_dp_matrices() of LPfold.c
• API: Fix z-score initialization in vrna_Lfoldz() amd vrna_mfe_window_zscore_cb()
• API: Fix file close issue in vrna_file_commands_read()
• API: Fix backtracking issue in Zuker subopt
• API: Fix missing soft constraints callback execution in Zuker subopt
• API: Fix enumeration of G-quadruplexes in vrna_subopt() and vrna_subopt_cb()
• API: Fix constraints bug for exterior loop in boltzmann sampling
• API: Allow for enforcing 'must pair' constraint (|) in dot-bracket constraints strings
• API: Fix discrepancy between global and local folding in how hard constraints for unpaired bases and non-specific pairing are applied
• API: Refactor function typdefs to make them actual function pointer typedefs
• SWIG: Fix Python 3 wrapper suffix issue
• SWIG: Fix Perl 5 wrapper for vrna_ud_prob_get()
• SWIG: Only accept upper triangular part of matrix input in fc.sc_bp_add()
• SWIG: Use var_array instead of tuples for Python RNA.ptable()
• SWIG: Add Python wrapper for vrna_move_neighbor_diff()
• SWIG: Add Python docstrings generated from doxygen documentation of C-library

Package

• Update libsvm to version 3.31
• Update dlib to version 19.24
• Adapt Debian dependencies
• Fix compilation issues with RNAforester
• AUTOCONF: Fix requirement checks when SVM support is deactivated and swig is missing
• AUTOMAKE: Add auto parameters for -flto compile/link flags
• AUTOCONF: Require C++17 due to dependencies to compile DLIB
• AUTOCONF: Deactivate Python 2 bindings by default

v2.5.1

This is version 2.5.1

v2.5.0

This is version 2.5.0

v2.4.18

This is version 2.4.18

v2.4.17

This is version 2.4.17

v2.4.16

This is version 2.4.16