| e7626aa | Ronny Lorenz | 07 June 2023, 17:48:50 UTC | MAN: Reorder --help and manpage sections | 07 June 2023, 17:48:50 UTC |
| 440a88e | Ronny Lorenz | 07 June 2023, 05:41:50 UTC | Add helical-rise and backbone-length options to executable programs | 07 June 2023, 05:42:21 UTC |
| ffdbbcc | Ronny Lorenz | 06 June 2023, 17:09:52 UTC | Resolve DNA specific setting for salt concentration dependence in executable programs that use old API | 06 June 2023, 21:00:47 UTC |
| 1aa75cd | Ronny Lorenz | 06 June 2023, 17:07:44 UTC | safeguard usage of md argument in gengetopt_helper for parameter file loading | 06 June 2023, 21:00:47 UTC |
| 9050a0e | Ronny Lorenz | 05 June 2023, 22:09:23 UTC | Make geometry constants part of vrna_md_t to remove global variables | 06 June 2023, 21:00:47 UTC |
| 4b5f95a | Hua-Ting Yao | 05 June 2023, 10:09:57 UTC | Make Backbone length global variable | 06 June 2023, 21:00:47 UTC |
| 3ba5597 | Ronny Lorenz | 06 June 2023, 21:00:33 UTC | Fix exterior loop constraints bug in boltzmann_sampling.c | 06 June 2023, 21:00:33 UTC |
| a0298cd | Ronny Lorenz | 06 June 2023, 19:32:31 UTC | Revisit hard constraints for sliding window predictions This should fix any potential issues and discrepancies betweem global and local folding predictions. In particular, the unpaired nucleotide and non-specific pairing constraints have been adapted. | 06 June 2023, 19:32:35 UTC |
| 85feb0e | Ronny Lorenz | 02 June 2023, 09:09:46 UTC | SWIG: Add typedefs.csv into distribution tarball | 04 June 2023, 10:08:08 UTC |
| 132f4d6 | Ronny Lorenz | 02 June 2023, 13:58:29 UTC | Refactor autoconf/automake rules for RNAxplorer man page | 04 June 2023, 10:07:55 UTC |
| bc62101 | Ronny Lorenz | 02 June 2023, 08:32:21 UTC | Add preliminary meta-data to dihydrouridine parameter file | 04 June 2023, 10:07:39 UTC |
| ad6609d | Ronny Lorenz | 02 June 2023, 07:43:27 UTC | Use dihydrouridine parameters from Rosetta/RECESS simulations instead of guesswork | 02 June 2023, 07:43:27 UTC |
| 6925440 | Ronny Lorenz | 02 June 2023, 07:17:35 UTC | Add JSON parameter file for Dihydrouridine | 02 June 2023, 07:17:35 UTC |
| ac46562 | Ronny Lorenz | 01 June 2023, 10:59:30 UTC | DOC: fix formula in comment of vrna_salt_ml() | 01 June 2023, 12:50:20 UTC |
| ce4d785 | Ronny Lorenz | 01 September 2022, 09:28:50 UTC | DOC: Add documentation for deprecated typedef `vrna_callback_free_auxdata` | 30 May 2023, 22:17:16 UTC |
| 405a806 | Ronny Lorenz | 30 July 2022, 13:52:47 UTC | Fix url in CONTRIBUTING.md | 30 May 2023, 22:16:26 UTC |
| a699beb | Ronny Lorenz | 30 May 2023, 21:37:07 UTC | DOC: Allow for deactivation of doxygen XML output This will also adapt the build process for the Python swig wrappers that usually expect doxy2swig generated docstrings which in turn depend on the doxygen XML output | 30 May 2023, 21:37:11 UTC |
| 5c2e35e | Ronny Lorenz | 30 May 2023, 20:18:30 UTC | SWIG: Wrap default model details constants | 30 May 2023, 20:18:30 UTC |
| 25c7232 | Ronny Lorenz | 30 May 2023, 20:09:57 UTC | SWIG: Allow for setting global salt correction variables | 30 May 2023, 20:09:57 UTC |
| 8081abe | Ronny Lorenz | 30 May 2023, 19:07:31 UTC | Enable change for salt duplex init correction factor | 30 May 2023, 19:42:50 UTC |
| 74c1210 | Hua-Ting Yao | 25 May 2023, 18:46:46 UTC | Use natural log in salt dependent uplex init correction | 30 May 2023, 19:42:34 UTC |
| e1ccda3 | Ronny Lorenz | 30 May 2023, 14:24:37 UTC | DOC: Replace travis badge by github workflow badge in README.md | 30 May 2023, 14:24:37 UTC |
| cd9ec0e | Ronny Lorenz | 30 May 2023, 13:55:32 UTC | DOC: Use static mathjax in Python documentation | 30 May 2023, 13:55:32 UTC |
| 5121cf2 | Ronny Lorenz | 30 May 2023, 13:54:13 UTC | SWIG: use full doxy2swig support for Python 2 interface | 30 May 2023, 13:54:13 UTC |
| 24ddf0c | Ronny Lorenz | 30 May 2023, 13:01:08 UTC | SWIG: doxy2swig.py: Enforce more numpy doc specifications in Python documentation | 30 May 2023, 13:01:08 UTC |
| cb1481c | Ronny Lorenz | 26 May 2023, 07:28:25 UTC | SWIG: Add .readthedocs.yaml for automatic build and upload of Python documentation | 30 May 2023, 06:35:35 UTC |
| d01cd3e | Ronny Lorenz | 26 May 2023, 07:11:52 UTC | DOC: Add first 'deprecated since version' tags to doxygen documentation | 30 May 2023, 06:35:35 UTC |
| be6e795 | Ronny Lorenz | 26 May 2023, 07:09:30 UTC | SWIG: Add typdef mapping for doxy2swig generated Python docstrings Also refactor deprecated sections to conform to numpy-style docstrings | 30 May 2023, 06:35:35 UTC |
| e5f8d0a | Ronny Lorenz | 23 May 2023, 14:43:27 UTC | SWIG: Add source files for Python module sphinx documentation | 30 May 2023, 06:35:35 UTC |
| 7dcc78d | Ronny Lorenz | 26 May 2023, 21:15:38 UTC | Add github release workflow | 29 May 2023, 22:09:05 UTC |
| 946a070 | Ronny Lorenz | 29 May 2023, 22:06:16 UTC | Remove .travis.yaml | 29 May 2023, 22:09:05 UTC |
| c4cf9ee | Ronny Lorenz | 29 May 2023, 16:11:59 UTC | Update CHANGELOG.md | 29 May 2023, 22:09:05 UTC |
| ffdf553 | Ronny Lorenz | 28 May 2023, 13:13:55 UTC | AUTOCONF: Add note about broken make distcheck for RNAforester | 28 May 2023, 13:14:30 UTC |
| 07cd481 | Ronny Lorenz | 28 May 2023, 12:01:01 UTC | change rm command in g2-0.72/demo/Makefile.in for clean rule | 28 May 2023, 13:14:30 UTC |
| a73c111 | Ronny Lorenz | 27 May 2023, 18:30:53 UTC | Fix cpp flags for python interface | 28 May 2023, 13:14:30 UTC |
| 1971d7a | Ronny Lorenz | 27 May 2023, 12:04:35 UTC | Fix duplicate VRNA_LIBS | 28 May 2023, 13:14:30 UTC |
| 54b7dc3 | Ronny Lorenz | 26 May 2023, 20:43:43 UTC | Add github issue template | 26 May 2023, 20:44:27 UTC |
| 387abb9 | Ronny Lorenz | 23 May 2023, 14:35:49 UTC | Add options parameter to vrna_sc_mod*() functions This allows one to specify whether any checks should be performed when preparing for modified parameter correction via the soft constraints framework, as well as whether warnings should be issued when checks fail. | 23 May 2023, 14:35:52 UTC |
| be03372 | Ronny Lorenz | 23 May 2023, 10:25:10 UTC | DOC: Refrain from using multiple @see,@note,etc. within the same documentation block This is mostly for downstream documentation post-processing, such as doxy2swig. | 23 May 2023, 10:25:13 UTC |
| cb67d3d | Ronny Lorenz | 23 May 2023, 10:23:03 UTC | SWIG: Silence doxy2swig and increase line wrapping to 100 chars | 23 May 2023, 10:23:03 UTC |
| fdb7242 | Ronny Lorenz | 23 May 2023, 10:22:12 UTC | DOC: Add formula support to doxy2swig.py | 23 May 2023, 10:22:12 UTC |
| 7eaa1e3 | Ronny Lorenz | 22 May 2023, 07:07:01 UTC | SWIG: Remove duplicates and add more function2method instructions to interfaces/classify.csv | 22 May 2023, 07:07:01 UTC |
| 7833401 | Ronny Lorenz | 22 May 2023, 07:04:36 UTC | DOC: Consistently use m as parameter name for vrna_move_t in ViennaRNA/landscape/move.h | 22 May 2023, 07:04:36 UTC |
| 4745d3c | Ronny Lorenz | 21 May 2023, 12:32:27 UTC | Print warning when deprecated read_parameter_file() function fails to parse parameters | 21 May 2023, 20:22:59 UTC |
| 032841c | Ronny Lorenz | 21 May 2023, 12:31:42 UTC | SWIG: Restructure Makefile.am for Python wrappers | 21 May 2023, 12:31:42 UTC |
| e4e4826 | Ronny Lorenz | 21 May 2023, 12:30:52 UTC | SWIG: Add more function2method instructions to interfaces/classify.csv | 21 May 2023, 12:30:52 UTC |
| dacba07 | Ronny Lorenz | 21 May 2023, 12:30:10 UTC | DOC: remove doxygen generated xml directory upon make maintainer-clean | 21 May 2023, 12:30:10 UTC |
| b8b56e8 | Ronny Lorenz | 21 May 2023, 12:29:16 UTC | DOC: add 'group' to compounddef parsing in doxy2swig | 21 May 2023, 12:29:35 UTC |
| 8b1e261 | Ronny Lorenz | 17 May 2023, 11:01:47 UTC | DOC: Fix classify.csv entries after changes in default vrna_fold_compound_t parameter names | 17 May 2023, 11:01:47 UTC |
| d57854f | Ronny Lorenz | 17 May 2023, 10:58:54 UTC | DOC: Consistently use fc as parameter name for vrna_fold_compound_t | 17 May 2023, 11:00:05 UTC |
| 37e9a8f | Ronny Lorenz | 17 May 2023, 07:10:30 UTC | update .gitignore in interfaces/Python* | 17 May 2023, 07:10:30 UTC |
| a9a1fac | Ronny Lorenz | 17 May 2023, 07:08:47 UTC | Rename classify.txt to classify.csv | 17 May 2023, 07:08:47 UTC |
| c589e94 | Ronny Lorenz | 11 May 2023, 10:05:27 UTC | DOC: Remove vrna_, VRNA_ and _t, _s, _e, _f prefixes and suffixes in Pythondoc generated by doxy2swig | 17 May 2023, 06:24:26 UTC |
| c788411 | Ronny Lorenz | 26 April 2023, 08:50:20 UTC | DOC: Convert more functions to methods in python doc string | 17 May 2023, 06:24:26 UTC |
| 86f5833 | Ronny Lorenz | 26 April 2023, 08:49:19 UTC | Fix open in doxy2swig for Python 2.7 | 17 May 2023, 06:24:26 UTC |
| 37c0b16 | Ronny Lorenz | 09 September 2022, 11:17:36 UTC | more changes in python docstring stuff | 17 May 2023, 06:24:26 UTC |
| bffdb69 | Ronny Lorenz | 30 July 2022, 13:51:40 UTC | SWIG: Add attribute lists and constructors to Python docstrings | 17 May 2023, 06:24:26 UTC |
| ac02dcc | Ronny Lorenz | 30 July 2022, 13:50:31 UTC | DOC: change attribute list output in doxy2swig.py | 17 May 2023, 06:24:26 UTC |
| c31a43f | Ronny Lorenz | 28 July 2022, 05:57:41 UTC | DOC: Start automatic build of python docstrings | 17 May 2023, 06:24:26 UTC |
| 95e81a4 | Ronny Lorenz | 28 July 2022, 05:55:56 UTC | DOC: extract parameter type for Python documentation | 17 May 2023, 06:24:26 UTC |
| 05cf1a8 | Ronny Lorenz | 25 July 2022, 09:34:47 UTC | DOC: doxy2swig fix when function2method wrapper input not available | 17 May 2023, 06:24:26 UTC |
| 25ab646 | Ronny Lorenz | 25 July 2022, 09:02:34 UTC | DOC: Add interfaces/classify.txt file that describes which functions are bound to which object in the SWIG interface | 17 May 2023, 06:24:26 UTC |
| 1b68c16 | Ronny Lorenz | 25 July 2022, 08:55:35 UTC | DOC: Activate doxygen XML output | 17 May 2023, 06:24:26 UTC |
| c077650 | Ronny Lorenz | 25 July 2022, 08:51:40 UTC | DOC: Minor changes and cleanup in parameter names in params.h | 17 May 2023, 06:24:26 UTC |
| c2da658 | Ronny Lorenz | 25 July 2022, 08:45:47 UTC | DOC: doxy2swig.py changes to print xrefsect | 17 May 2023, 06:24:26 UTC |
| 4d0118c | Ronny Lorenz | 25 July 2022, 08:45:17 UTC | DOC: doxy2swig.py changes to properly print Notes sections | 17 May 2023, 06:24:26 UTC |
| aa876db | Ronny Lorenz | 25 July 2022, 08:44:30 UTC | DOC: doxy2swig.py changes to allow for binding functions as object methods | 17 May 2023, 06:24:26 UTC |
| 45775c0 | Ronny Lorenz | 25 July 2022, 08:40:08 UTC | DOC: Add doxy2swig.py script | 17 May 2023, 06:24:26 UTC |
| a721742 | Ronny Lorenz | 16 May 2023, 11:48:02 UTC | SWIG: Add low-level function wrappers for salt correction | 16 May 2023, 11:57:14 UTC |
| f624ba6 | Ronny Lorenz | 16 May 2023, 09:55:00 UTC | Change helical rise parameter depending on whether RNA or DNA parameters are loaded | 16 May 2023, 09:55:00 UTC |
| e1dae1f | Ronny Lorenz | 12 May 2023, 16:45:22 UTC | Make helical rise as used for salt corrections a variable | 12 May 2023, 16:51:42 UTC |
| cb3cb0c | Ronny Lorenz | 12 May 2023, 15:02:34 UTC | SWIG: Add wrapper connect (CT) format parser | 12 May 2023, 15:02:34 UTC |
| 2036ab3 | Ronny Lorenz | 16 May 2019, 16:45:42 UTC | Add RNAstrand Dot-parenthesis input file parser | 12 May 2023, 11:38:08 UTC |
| d3ab20a | Ronny Lorenz | 10 May 2023, 19:46:51 UTC | DOC: Update CHANGELOG.md | 10 May 2023, 19:46:51 UTC |
| c68791a | Ronny Lorenz | 10 May 2023, 17:09:52 UTC | DOC: Add documentation for dot-plot creating functions | 10 May 2023, 17:09:52 UTC |
| cce3e22 | Ronny Lorenz | 05 May 2023, 11:11:20 UTC | Fix default value for RNAinverse -R option in help and manpage | 05 May 2023, 11:11:20 UTC |
| 8032628 | Ronny Lorenz | 04 May 2023, 12:49:04 UTC | Fix missing strand separators for multiple interacting input sequences in vrna_subopt() and RNAsubopt | 04 May 2023, 12:49:04 UTC |
| 5d11be5 | Ronny Lorenz | 03 May 2023, 14:18:18 UTC | Allow for only -Fp in RNAinverse instead of always assuming -Fm | 03 May 2023, 14:18:18 UTC |
| d7168fe | Ronny Lorenz | 03 May 2023, 14:01:50 UTC | Introduce and use fallback base for modified positions without energy parameters | 03 May 2023, 14:01:50 UTC |
| 9285d58 | Ronny Lorenz | 25 April 2023, 22:14:48 UTC | Fix vrna_subopt() and RNAsubopt sorted output with G-quadruplexes | 25 April 2023, 22:14:48 UTC |
| 764394a | Ronny Lorenz | 25 April 2023, 21:47:15 UTC | AUTOCONF: Change RNAlib compile/link flag variables to adjust for integration as ViennaRNA subpackage | 25 April 2023, 21:47:15 UTC |
| dc5b93d | Ronny Lorenz | 31 March 2023, 11:16:06 UTC | Fix enumeration of gquads in subopt | 25 April 2023, 18:58:45 UTC |
| 4e49747 | Ronny Lorenz | 24 April 2023, 10:01:03 UTC | SWIG: Deactivate new vrna_ptable objects in Perl 5 | 24 April 2023, 10:03:18 UTC |
| 01891c0 | Ronny Lorenz | 04 March 2023, 20:51:01 UTC | TESTS: Hack ptable access in Per5 tests -> needs attention! | 24 April 2023, 10:03:18 UTC |
| efa412e | Ronny Lorenz | 27 December 2022, 20:08:33 UTC | Next step for new ptable swig wrapper | 24 April 2023, 10:03:18 UTC |
| a214c1a | Ronny Lorenz | 03 October 2022, 07:50:02 UTC | SWIG: Add wrapper for vrna_move_neighbor_diff() | 24 April 2023, 10:03:18 UTC |
| 907387e | Ronny Lorenz | 02 October 2022, 14:23:31 UTC | SWIG: Allow for var_array<short> input in functions/methods operating on pair tables | 24 April 2023, 10:03:18 UTC |
| 3ab611c | Ronny Lorenz | 26 September 2022, 21:39:25 UTC | Create var_array instead of tuple for RNA.ptable() | 24 April 2023, 10:03:18 UTC |
| 804aab0 | Ronny Lorenz | 19 April 2023, 12:16:15 UTC | Add modified base support to RNAsubopt | 20 April 2023, 20:04:54 UTC |
| 9c96b0f | Ronny Lorenz | 19 April 2023, 08:52:02 UTC | Add modified bases support to RNAcofold | 20 April 2023, 20:04:54 UTC |
| c864b5b | Ronny Lorenz | 18 April 2023, 22:59:31 UTC | Add modified bases support to RNAplfold | 20 April 2023, 20:04:54 UTC |
| 62ffc0d | Ronny Lorenz | 18 April 2023, 22:59:12 UTC | Add modified bases support to RNALfold | 20 April 2023, 20:04:54 UTC |
| 0a1ad55 | Ronny Lorenz | 18 April 2023, 16:37:34 UTC | MAN: Add modified base options and re-order RNAplfold command line options | 20 April 2023, 20:04:54 UTC |
| c5961e7 | Ronny Lorenz | 18 April 2023, 16:37:25 UTC | MAN: Add modified base options and re-order RNALfold command line options | 20 April 2023, 20:04:54 UTC |
| 32a8e72 | Ronny Lorenz | 18 April 2023, 15:40:33 UTC | MAN: Re-order RNAfold command line options as shown by --help or within manpage | 20 April 2023, 20:04:54 UTC |
| 5087afa | Ronny Lorenz | 18 April 2023, 15:20:22 UTC | MAN: Add example for modified bases support in RNAfold manpage | 20 April 2023, 20:04:54 UTC |
| d91c51d | Ronny Lorenz | 18 April 2023, 08:46:34 UTC | Factor-out modified base support functions for re-use in executable wrappres | 20 April 2023, 20:04:54 UTC |
| 58eea02 | Ronny Lorenz | 18 April 2023, 07:42:50 UTC | First draft for RNAfold with modified base support | 20 April 2023, 20:04:54 UTC |
| 4814a01 | Ronny Lorenz | 18 April 2023, 07:39:53 UTC | Add vrna_strchr() function | 20 April 2023, 20:04:54 UTC |
| c07b268 | Ronny Lorenz | 17 April 2023, 12:08:29 UTC | Use 9 as one-letter code for Purine aka nebularine | 20 April 2023, 20:04:54 UTC |
