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tzok / rnapolis-py

A Python library containing RNA-related bioinformatics functions and classes.
MIT License
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build: bump viennarna from 2.6.4 to 2.7.0 #247

Closed dependabot[bot] closed 1 month ago

dependabot[bot] commented 1 month ago

Bumps viennarna from 2.6.4 to 2.7.0.

Release notes

Sourced from viennarna's releases.

ViennaRNA Package 2.7.0

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

... (truncated)

Changelog

Sourced from viennarna's changelog.

Version 2.7.0

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

... (truncated)

Commits
  • 43fd082 Fix stand-alone python builds
  • dbb0ea8 RTD: Fix automatic build for readthedocs.io
  • c20559f WORKFLOWS: Deactivate build of osx installer for now
  • a093387 WORKFLOWS: Fix osx installer uploda/download for release
  • e81d230 WORKFLOWS: Fix release workflow dependency (again)
  • 1d5a750 WORKFLOWS: Fix svm version in workflow files
  • a422d4a WORKFLOWS: Fix release workflow dependency
  • 3c2dac0 Prepare for release of ViennaRNA v2.7.0
  • 29896a6 WORKFLOWS: Setup MacOS X build for x86_64 and ARM
  • 3977295 Fix access to f3 DP matrices for sliding-window MFE exterior loop
  • Additional commits viewable in compare view


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