ViennaRNA 2.7.1__tar.gz → 2.7.2__tar.gz

{viennarna-2.7.1 → viennarna-2.7.2}/CHANGELOG.md

@@ -5,7 +5,28 @@ Below, you'll find a list of notable changes for each version of the ViennaRNA P
 ## Version 2.7.x
 
 
-### [Unreleased](https://github.com/ViennaRNA/ViennaRNA/compare/v2.7.1...HEAD)
+### [Unreleased](https://github.com/ViennaRNA/ViennaRNA/compare/v2.7.2...HEAD)
+
+
+### [Version 2.7.2](https://github.com/ViennaRNA/ViennaRNA/compare/v2.7.1...v2.7.2)
+
+#### 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
 
 
 ### [Version 2.7.1](https://github.com/ViennaRNA/ViennaRNA/compare/v2.7.0...v2.7.1)

{viennarna-2.7.1 → viennarna-2.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ViennaRNA
-Version: 2.7.1
+Version: 2.7.2
 Summary: A library for the prediction and comparison of RNA secondary structures.
 Author-email: Ronny Lorenz <ronny@tbi.univie.ac.at>, "Ivo L. Hofacker" <ivo@tbi.univie.ac.at>
 Maintainer-email: Ronny Lorenz <rna@tbi.univie.ac.at>, Ayaan Hossain <auh57@psu.edu>
@@ -122,8 +122,8 @@ and installation process.*
 
 Usually you'll simply unpack the distribution tarball, configure and make:
 ```
-tar -zxvf ViennaRNA-2.7.1.tar.gz
-cd ViennaRNA-2.7.1
+tar -zxvf ViennaRNA-2.7.2.tar.gz
+cd ViennaRNA-2.7.2
 ./configure
 make
 sudo make install

{viennarna-2.7.1 → viennarna-2.7.2}/README.md

@@ -88,8 +88,8 @@ and installation process.*
 
 Usually you'll simply unpack the distribution tarball, configure and make:
 ```
-tar -zxvf ViennaRNA-2.7.1.tar.gz
-cd ViennaRNA-2.7.1
+tar -zxvf ViennaRNA-2.7.2.tar.gz
+cd ViennaRNA-2.7.2
 ./configure
 make
 sudo make install

{viennarna-2.7.1 → viennarna-2.7.2}/ViennaRNA.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ViennaRNA
-Version: 2.7.1
+Version: 2.7.2
 Summary: A library for the prediction and comparison of RNA secondary structures.
 Author-email: Ronny Lorenz <ronny@tbi.univie.ac.at>, "Ivo L. Hofacker" <ivo@tbi.univie.ac.at>
 Maintainer-email: Ronny Lorenz <rna@tbi.univie.ac.at>, Ayaan Hossain <auh57@psu.edu>
@@ -122,8 +122,8 @@ and installation process.*
 
 Usually you'll simply unpack the distribution tarball, configure and make:
 ```
-tar -zxvf ViennaRNA-2.7.1.tar.gz
-cd ViennaRNA-2.7.1
+tar -zxvf ViennaRNA-2.7.2.tar.gz
+cd ViennaRNA-2.7.2
 ./configure
 make
 sudo make install

{viennarna-2.7.1 → viennarna-2.7.2}/ViennaRNA.egg-info/SOURCES.txt

@@ -258,6 +258,7 @@ src/ViennaRNA/loops/hairpin.h
 src/ViennaRNA/loops/internal.h
 src/ViennaRNA/loops/multibranch.h
 src/ViennaRNA/math/fun_bin.c
+src/ViennaRNA/math/fun_chain.c
 src/ViennaRNA/math/fun_gaussian.c
 src/ViennaRNA/math/fun_kde.c
 src/ViennaRNA/math/fun_linear.c
@@ -384,10 +385,13 @@ src/ViennaRNA/probing/SHAPE.c
 src/ViennaRNA/probing/SHAPE.h
 src/ViennaRNA/probing/basic.h
 src/ViennaRNA/probing/probing.c
+src/ViennaRNA/probing/strategy_chain.c
 src/ViennaRNA/probing/strategy_deigan.c
 src/ViennaRNA/probing/strategy_deigan.h
 src/ViennaRNA/probing/strategy_eddy.c
 src/ViennaRNA/probing/strategy_eddy.h
+src/ViennaRNA/probing/strategy_nlogp.c
+src/ViennaRNA/probing/strategy_nlogp.h
 src/ViennaRNA/probing/strategy_zarringhalam.c
 src/ViennaRNA/probing/strategy_zarringhalam.h
 src/ViennaRNA/sampling/basic.h

{viennarna-2.7.1 → viennarna-2.7.2}/config.h

@@ -154,7 +154,7 @@
 #define PACKAGE_NAME "ViennaRNA"
 
 /* Define to the full name and version of this package. */
-#define PACKAGE_STRING "ViennaRNA 2.7.1"
+#define PACKAGE_STRING "ViennaRNA 2.7.2"
 
 /* Define to the one symbol short name of this package. */
 #define PACKAGE_TARNAME "ViennaRNA"
@@ -163,7 +163,7 @@
 #define PACKAGE_URL "https://www.tbi.univie.ac.at/RNA"
 
 /* Define to the version of this package. */
-#define PACKAGE_VERSION "2.7.1"
+#define PACKAGE_VERSION "2.7.2"
 
 /* Define to necessary symbol if this constant uses a non-standard name on
    your system. */
@@ -269,7 +269,7 @@
 
 
 /* Version number of package */
-#define VERSION "2.7.1"
+#define VERSION "2.7.2"
 
 /* Do not log debug messages within RNAlib code */
 //#define VRNA_LOG_NO_DEBUG_RNALIB 1
@@ -281,7 +281,7 @@
 /* #undef VRNA_NR_SAMPLING_MPFR */
 
 /* version of ViennaRNA Package */
-#define VRNA_VERSION "2.7.1"
+#define VRNA_VERSION "2.7.2"
 
 /* Warn upon usage of deprecated symbols */
 /* #undef VRNA_WARN_DEPRECATED */

{viennarna-2.7.1 → viennarna-2.7.2}/interfaces/Python/RNA/RNA.py

@@ -190,7 +190,7 @@ def cdata(ptr, nelements=1):
 def memmove(data, indata):
     return _RNA.memmove(data, indata)
 
-__version__ = '2.7.1'
+__version__ = '2.7.2'
 
 class SwigPyIterator(object):
     thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
@@ -2068,7 +2068,7 @@ class basepair(object):
 
     Typename for base pair element.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.bp() instead!  
 
     Attributes
@@ -2090,7 +2090,7 @@ class basepair(object):
 
         Typename for base pair element.  
 
-        .. deprecated:: 2.7.1
+        .. deprecated:: 2.7.2
             Use RNA.bp() instead!  
 
         Attributes
@@ -2451,7 +2451,7 @@ class exp_param(object):
     id : int  
         An identifier for the data structure.  
 
-        .. deprecated:: 2.7.1
+        .. deprecated:: 2.7.2
             This attribute will be removed in version 3  
 
     expstack : double  
@@ -2624,7 +2624,7 @@ class exp_param(object):
         id : int  
             An identifier for the data structure.  
 
-            .. deprecated:: 2.7.1
+            .. deprecated:: 2.7.2
                 This attribute will be removed in version 3  
 
         expstack : double  
@@ -3149,7 +3149,7 @@ def read_parameter_file(fname):
 
     Read energy parameters from a file.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.params_load() instead!  
 
     Parameters
@@ -3166,7 +3166,7 @@ def write_parameter_file(fname):
 
     Write energy parameters to a file.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.params_save() instead!  
 
     Parameters
@@ -5141,7 +5141,7 @@ class score(object):
     F1 = property(_RNA.score_F1_get, _RNA.score_F1_set)
     MCC = property(_RNA.score_MCC_get, _RNA.score_MCC_set)
 
-    def __init__(self, TP=0, TN=0, FP=0, FN=0):
+    def __init__(self, TP=0., TN=0., FP=0., FN=0.):
         _RNA.score_swiginit(self, _RNA.new_score(TP, TN, FP, FN))
 
     def __str__(self):
@@ -6416,7 +6416,7 @@ def simple_xy_coordinates(*args):
 
     Calculate nucleotide coordinates for secondary structure plot the *Simple way*.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Consider switching to RNA.plot_coords_simple_pt() instead!  
 
     See Also
@@ -6624,7 +6624,7 @@ def PS_rna_plot(string, structure, file):
 
     Produce a secondary structure graph in PostScript and write it to 'filename'.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.file_PS_rnaplot() instead!  
 
     """
@@ -6637,7 +6637,7 @@ def PS_rna_plot_a(string, structure, file, pre, post):
     Produce a secondary structure graph in PostScript including additional annotation macros and write
     it to 'filename'.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.file_PS_rnaplot_a() instead!  
 
     """
@@ -6650,7 +6650,7 @@ def PS_rna_plot_a_gquad(string, structure, ssfile, pre, post):
     Produce a secondary structure graph in PostScript including additional annotation macros and write
     it to 'filename' (detect and draw g-quadruplexes).  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.file_PS_rnaplot_a() instead!  
 
     """
@@ -6818,7 +6818,7 @@ def PS_dot_plot(string, file):
     The "dot plot" represents each base pairing probability by a square of corresponding area in a
     upper triangle matrix. The lower part of the matrix contains the minimum free energy  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function is deprecated and will be removed soon! Use PS_dot_plot_list() instead!  
 
     Note
@@ -8247,7 +8247,7 @@ def energy_of_structure(string, structure, verbosity_level):
 
     If verbosity level is set to a value >0, energies of structure elements are printed to stdout  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.eval_structure() or RNA.fold_compound.eval_structure_verbose() instead!  
 
     Note
@@ -8290,7 +8290,7 @@ def energy_of_circ_structure(string, structure, verbosity_level):
     OpenMP: This function relies on several global model settings variables and thus is not to be
     considered threadsafe. See energy_of_circ_struct_par() for a completely threadsafe implementation.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.eval_structure() or RNA.fold_compound.eval_structure_verbose() instead!  
 
     Parameters
@@ -8329,7 +8329,7 @@ def energy_of_structure_pt(string, ptable, s, s1, verbosity_level):
 
     If verbosity level is set to a value >0, energies of structure elements are printed to stdout  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.eval_structure_pt() or RNA.fold_compound.eval_structure_pt_verbose()
         instead!  
 
@@ -8372,7 +8372,7 @@ def energy_of_move(string, structure, m1, m2):
     If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is
     insertion (opening).  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.eval_move() instead!  
 
     Parameters
@@ -8407,7 +8407,7 @@ def energy_of_move_pt(pt, s, s1, m1, m2):
     If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is
     insertion (opening).  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.eval_move_pt() instead!  
 
     Parameters
@@ -8441,7 +8441,7 @@ def loop_energy(ptable, s, s1, i):
 
     Calculate energy of a loop.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.eval_loop_pt() instead!  
 
     Parameters
@@ -8473,7 +8473,7 @@ def energy_of_struct(string, structure):
 
     Calculate the free energy of an already folded RNA  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function is deprecated and should not be used in future programs! Use energy_of_structure()
         instead!  
 
@@ -8507,7 +8507,7 @@ def energy_of_struct_pt(string, ptable, s, s1):
 
     Calculate the free energy of an already folded RNA  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function is deprecated and should not be used in future programs! Use
         energy_of_structure_pt() instead!  
 
@@ -8545,7 +8545,7 @@ def energy_of_circ_struct(string, structure):
 
     Calculate the free energy of an already folded circular RNA  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function is deprecated and should not be used in future programs Use
         energy_of_circ_structure() instead!  
 
@@ -8604,7 +8604,7 @@ def E_Stem(type, si1, sj1, extLoop, P):
     number to both, si1 and sj1. In case the argument extLoop is 0, the returned energy contribution
     also includes the *internal-loop-penalty* of a multiloop stem with closing pair type.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Please use one of the functions RNA.E_exterior_stem() and RNA.E_multibranch_stem() instead!
         Use the former for cases where `extLoop` != 0 and the latter otherwise.  
 
@@ -8650,7 +8650,7 @@ def exp_E_ExtLoop(type, si1, sj1, P):
 
     This is the partition function variant of E_ExtLoop()  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.exp_E_ext_stem() instead!  
 
     Returns
@@ -9095,7 +9095,7 @@ def cofold(*args):
     recursively filled matrices are not available any more for any post-processing, e.g. suboptimal
     backtracking, etc.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function is obsolete since RNA.mfe()/RNA.fold() can handle complexes multiple sequences
         since v2.5.0. Use RNA.mfe()/RNA.fold() for connected component MFE instead and compute MFEs of
         unconnected states separately.  
@@ -9253,7 +9253,7 @@ def free_arrays():
 
     Free arrays for mfe folding.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         See RNA.fold(), RNA.circfold(), or RNA.fold_compound.mfe() and RNA.fold_compound() for the usage
         of the
         new API!  
@@ -9267,7 +9267,7 @@ def update_fold_params():
 
     Recalculate energy parameters.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         For non-default model settings use the new API with RNA.fold_compound.params_subst() and
         RNA.fold_compound.mfe() instead!  
 
@@ -9281,7 +9281,7 @@ def circalifold(*args):
     Compute MFE and according structure of an alignment of sequences assuming the sequences are circular
     instead of linear.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Usage of this function is discouraged! Use RNA.alicircfold(), and RNA.fold_compound.mfe()
         instead!  
 
@@ -9311,7 +9311,7 @@ def free_alifold_arrays():
 
     Free the memory occupied by MFE alifold functions.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Usage of this function is discouraged! It only affects memory being free'd that was allocated by
         an old API function before. Release of memory occupied by the newly introduced
         RNA.fold_compound() is handled by RNA.fold_compound_free()  
@@ -9329,7 +9329,7 @@ def free_co_arrays():
 
     Free memory occupied by cofold().  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function will only free memory allocated by a prior call of cofold() or cofold_par(). See
         RNA.fold_compound.mfe_dimer() for how to use the new API  
 
@@ -9350,7 +9350,7 @@ def update_cofold_params():
 
     Recalculate parameters.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         See RNA.fold_compound.params_subst() for an alternative using the new API  
 
     """
@@ -9362,7 +9362,7 @@ def initialize_cofold(length):
 
     allocate arrays for folding  
 
-    .. deprecated:: 2.7.1  
+    .. deprecated:: 2.7.2  
 
     """
     return _RNA.initialize_cofold(length)
@@ -9608,7 +9608,7 @@ def pbacktrack_circ(sequence):
         st_back has to be set to 1 before calling pf_fold() or pf_fold_par()  pf_fold_par() or
         pf_circ_fold() have to be called first to fill the partition function matrices  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.pbacktrack() instead.  
 
     Parameters
@@ -9633,7 +9633,7 @@ def free_pf_arrays():
     Call this function if you want to free all allocated memory associated with the partition function
     forward recursion.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         See RNA.fold_compound() and its related functions for how to free memory occupied by the
         dynamic programming matrices  
 
@@ -9662,7 +9662,7 @@ def update_pf_params(length):
     Call this function to recalculate the pair matrix and energy parameters after a change in folding
     parameters like temperature  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.exp_params_subst() instead  
 
     """
@@ -9674,7 +9674,7 @@ def mean_bp_distance(length):
 
     Get the mean base pair distance of the last partition function computation.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.mean_bp_distance() or RNA.mean_bp_distance_pr() instead!  
 
     Parameters
@@ -9699,7 +9699,7 @@ def init_pf_fold(length):
 
     Allocate space for pf_fold().  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function is obsolete and will be removed soon!  
 
     """
@@ -9716,7 +9716,7 @@ def centroid(length, dist):
     r"""
 
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function is deprecated and should not be used anymore as it is not threadsafe!  
 
     See Also
@@ -9735,7 +9735,7 @@ def free_co_pf_arrays():
 
     Free the memory occupied by co_pf_fold().  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function will be removed for the new API soon! See RNA.fold_compound.pf_dimer(),
         RNA.fold_compound(),
         and RNA.fold_compound_free() for an alternative  
@@ -9751,7 +9751,7 @@ def update_co_pf_params(length):
 
     This function recalculates all energy parameters given the current model settings.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.fold_compound.exp_params_subst() instead!  
 
     Parameters
@@ -9798,7 +9798,7 @@ def get_centroid_struct_pl(length, dist, pl):
 
     Get the centroid structure of the ensemble.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function was renamed to RNA.centroid_from_plist()  
 
     """
@@ -9810,7 +9810,7 @@ def get_centroid_struct_pr(length, dist, pr):
 
     Get the centroid structure of the ensemble.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function was renamed to RNA.centroid_from_probs()  
 
     """
@@ -10288,7 +10288,7 @@ def zukersubopt(string):
     energy structure containing the resp. base pair. Returns a list of these structures and their
     energies.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         use RNA.zukersubopt() instead  
 
     Parameters
@@ -10366,7 +10366,7 @@ def b2HIT(structure):
 
     Converts the full structure from bracket notation to the HIT notation including root.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         See RNA.db_to_tree_string() and RNA.STRUCTURE_TREE_HIT for a replacement  
 
     Parameters
@@ -10387,7 +10387,7 @@ def b2C(structure):
     Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B'
     'I' 'M' and 'R' identifiers.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         See RNA.db_to_tree_string() and RNA.STRUCTURE_TREE_SHAPIRO_SHORT for a replacement  
 
     Parameters
@@ -10408,7 +10408,7 @@ def b2Shapiro(structure):
     Converts the full structure from bracket notation to the *weighted* coarse grained notation using
     the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         See RNA.db_to_tree_string() and RNA.STRUCTURE_TREE_SHAPIRO_WEIGHT for a replacement  
 
     Parameters
@@ -10694,7 +10694,7 @@ def Make_bp_profile(length):
     r"""
 
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function is deprecated and will be removed soon! See Make_bp_profile_bppm() for a
         replacement  
 
@@ -10942,7 +10942,7 @@ def read_record(header, sequence, rest, options):
 
     Get a data record from stdin.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         This function is deprecated! Use RNA.file_fasta_read_record() as a replacment.  
 
     """
@@ -12220,7 +12220,7 @@ def find_saddle(seq, s1, s2, width):
 
     Find energy of a saddle point between 2 structures (search only direct path).  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.path_findpath_saddle() instead!  
 
     Parameters
@@ -12250,7 +12250,7 @@ def free_path(path):
 
     Free memory allocated by get_path() function.  
 
-    .. deprecated:: 2.7.1
+    .. deprecated:: 2.7.2
         Use RNA.path_free() instead!  
 
     Parameters
@@ -12686,7 +12686,7 @@ class fold_compound(object):
     ptype_pf_compat : char *  
         ptype array indexed via iindx  
 
-        .. deprecated:: 2.7.1
+        .. deprecated:: 2.7.2
             This attribute will vanish in the future! It's meant for backward compatibility only!  
 
         Warnings
@@ -12796,7 +12796,7 @@ class fold_compound(object):
     pscore_pf_compat : short *  
         Precomputed array of pair types expressed as pairing scores indexed via iindx.  
 
-        .. deprecated:: 2.7.1
+        .. deprecated:: 2.7.2
             This attribute will vanish in the future!  
 
         Warnings
@@ -14490,7 +14490,7 @@ class fold_compound(object):
 
         The code is analog to the RNA.fold_compound.mfe() function.  
 
-        .. deprecated:: 2.7.1
+        .. deprecated:: 2.7.2
             This function is obsolete since RNA.fold_compound.mfe() can handle complexes multiple sequences
             since v2.5.0.
             Use RNA.fold_compound.mfe() for connected component MFE instead and compute MFEs of unconnected

{viennarna-2.7.1 → viennarna-2.7.2}/interfaces/Python/RNA/__init__.py

@@ -35,7 +35,7 @@ Amongst other things, our implementations allow you to:
 - predict interactions between multiple RNA molecules
 '''
 
-__version__ = '2.7.1'
+__version__ = '2.7.2'
 
 __author__ = 'Ronny Lorenz <rna@tbi.univie.ac.at>'