Programs

• Fix structure output in RNAeval for more than 2 interacting RNAs
• Fix wrong application of soft constraints to single sequences in RNAcofold
• Add --benchmark option for RNAfold
• Add --benchmark option for RNAalifold

Library

• API: Fix wrong application of soft constraints to single sequences in vrna_mfe_dimer()
• API: Restore backward compatibility issues after early removal of vrna_constraints_add_SHAPE() and others
• API: Re-use energy parameters for successive vrna_params() / vrna_exp_params() calls if possible
• API: Add negative log probability method (information content) as generic probing data strategy
• API: Add vrna_math_dbl_chain() to allow for chaining vrna_math_dbl* functions
• API: Add function to allow for chaining probing data strategies
• API: Change structure benchmark numbers to double type

Package

• Fix misplaced 'i' in rna_turner2004.par

Programs

• Allow for FASTA header changes in ct2db
• Fix constraints parsing in RNAsubopt
• Add new command line options for structure probing data to RNAfold and RNAsubopt

Library

• API: Refactor structure probing data API to support multiple data at once, position-wise weighting, user-defined reactivity-to-energy strategies and more
• API: Refactor hard constraint wrappers
• API: Add ViennaRNA/math/ to provide several useful mathematical functions
• API: Add vrna_str_to_dbl_array()
• API: Add vrna_file_doubles_read()
• API: Fix backtracking issues in exterior loop
• API: Fix backtracking issues with odd dangles
• API: Fix segmentation fault in vrna_pt_pk_remove()
• API: Fix vrna_plist() and vrna_ptable() to deal with malformed input
• API: Fix soft constraints access in backtracking of QM2 (Boltzmann sampling)
• SWIG: Add wrappers for concentration dependency computations
• SWIG: Fix RNA.fold_compound.bpp() output for multistrand base pair probabilities
• SWIG: Do not return symmetric pair probability matrix by default
• SWIG: Fix Python object ownership in callbacks for unstructured domains, direct soft constraints and landscape moves

Package

• Update dlib to version 20.0
• Overall improvements to the documentation
• Fix energy parameter file markup
• Fix compilation with compilers that default to C23
• Update swig requirement to 4.2.0
• Fix compilation without libsvm
• Update breathe to version v5.0.0a5
• Add probing data priors (paired and unpaired) for 1M7 and DMS

Programs

• Add hard limit for number of input structures in RNAdistance
• Add counter example settings to RNAalifold
• Add covariance annotation legend to RNAplot layout plots for MSA input
• Add covariance annotation legend to RNALalifold layout plots
• Adapt structure conservation coloring and add legend in alignment output of RNAplot, RNAalifold, and RNALalifold
• Add RNAconsensus Python program that will eventually replace refold.pl
• Add --log-file, --log-level, --log-call and --log-time command line options to executable programs
• Add --betaScale and --pfScale options to and rescale Boltzmann factors in RNAPKplex
• Add support for G-Quadruplexes in circular RNAs for RNAfold, RNAalifold, and RNAeval
• Change RNAplot command line argument -o to -f
• Add --random-seed option to RNAsubopt and RNAalifold to specify seed for random number generator

Library

• API: Add circular RNA G-Quadruplex support
• API: Add structure prediction benchmark functions vrna_compare_structure() and vrna_compare_structure_pt()
• API: Add vrna_annotate_covar_pt() that allows for specifying number of counter examples
• API: Add structure conservation legend to EPS consensus structure layout plots
• API: Add vrna_string_make_space_for() and vrna_string_available_space() functions in ViennaRNA/datastructures/string.h
• API: Add vrna_file_PS_aln_opt() to allow for changing conservation coloring
• API: Add flexible log message system to avoid spam on stderr and stdout
• API: Add (generic) compressed sparse row (CSR) matrix implementation
• API: Add Eddy 2014 approach to incorporate experimental probing data (using Gaussian KDE)
• API: Add generic support for experimental probing data via new API in ViennaRNA/probing/basic.h
• API: Add full probing data support for consensus structure prediction
• API: Add vrna_sc_multi_cb_add_comparative() to allow for multi callback soft constraints in comparative structure predictions
• API: Add vrna_fold_compound_t to parameters passed to recursion status callback
• API: Add M2 matrices in favor of M1 for global MFE and partition function computations
• API: Add safeguard to vrna_array_free()
• API: Add vrna_pairing_tendency() as replacement for vrna_db_from_probs()
• API: Group related API symbols and header files into specific subdirectories
• API: Allow base pair hard constraints via commands file where j = i + 1
• API: Refactor vrna_pk_plex() accessibility computations
• API: Refactor backtracking implementations and API, now located under ViennaRNA/backtrack/
• API: Refactor experimental probing data (SHAPE) implementations, now located under ViennaRNA/probing/
• API: Refactor auxiliary grammar extension API, now located under ViennaRNA/grammar/
• API: Refactor G-Quadruplex implementation and fix existing bugs and numerical issues in corresponding energy evaluation
• API: Refactor verbose vrna_eval*() implementations
• API: Refactor structure plotting API and add unified structure plotting function vrna_plot_structure()
• API: Remove exit() calls from RNAlib
• API: Change behavior and parameter order for vrna_hc_add_bp_strand()
• API: Change behavior and parameters of vrna_hc_add_up_strand()
• API: Unify backtracking matrix flags
• API: Use vrna_array() based base pair and backtrack stacks for MFE implementations
• API: Introduce entropic penalty for unpaired circular RNAs (may be switched off by model settings circ_penalty flag)
• API: Deprecate vrna_message_info(), vrna_message_warning(), and vrna_message_error() in favor of new loggin system
• API: Fix vrna_neighbor_diff*() insertion moves
• API: Fix MFE inside recursion for multiloop unpaired positions
• API: Fix vrna_hx_from_ptable() when provided hairpins of length 0
• API: Fix vrna_hx_merge() to support pseudoknotted helices
• API: Fix re-use of previous energy parameters upon model changes in duplex.c
• API: Fix re-use of previous energy parameters upon model changes in c_plex.c
• API: Fix re-use of previous energy parameters upon model changes in plex.c
• API: Fix re-use of previous energy parameters upon model changes in ali_plex.c
• API: Fix re-use of previous energy parameters upon model changes in snofold.c
• API: Fix re-use of previous energy parameters upon model changes in snoop.c
• API: Fix mismatch and dangling end energies in sc_cb_mod.c for modified base support
• API: Fix Zuker-style subopt backtracking
• API: Fix bug in vrna_strdup_vprintf() that resulted in losing parmeters upon consecutive calls
• API: Fix default exterior loop MFE soft constraints for comparative structure prediction
• SWIG: Use av_len() instad of av_top_index() for Perl 5 to support perl5 < v5.18.0
• SWIG: Fix compilation issues for Python 3.12 due to use of SWIG_Python_str_AsChar()
• SWIG: Add wrapper for vrna_hx_merge()
• SWIG: Add wrapper for vrna_sc_multi_cb_add()
• SWIG: Add wrappers for vrna_hc_add_bp_strand() and vrna_hc_add_up_strand()
• SWIG: Add file I/O constants
• SWIG: Add wrappers for structure prediction benchmark functions
• SWIG: Add wrappers for log message system
• SWIG: Add wrapper for vrna_stack_prob()
• SWIG: Add wrappers for new probing data API
• SWIG: Add wrapper for vrna_n_multichoose_k()
• SWIG: Return int instead of float for eval_structure_pt_simple()

Package

• AUTOCONF: Fix several autoconf/automake related issues
• AUTOCONF: Add ./configure --enable-debug option that prevents removal of vrna_log_debug() message from RNAlib
• Add m5C JSON energy parameter file
• Add N1-methylpseudouridine JSON energy parameter file
• Add OpenMP library flags to RNAlib2.pc
• DOC: Improve document structure
• Bump libsvm to version 3.35
• Remove RNA-Tutorial since it is now included as part of the reference manual
• Remove Python 2 builds from MacOSX installer

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

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

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

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

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