| ecb70c3 | Ronny Lorenz | 12 June 2023, 06:49:30 UTC | Prepare for release v2.6.1 | 12 June 2023, 09:34:31 UTC |
| 6bfdaec | Ronny Lorenz | 12 June 2023, 06:43:34 UTC | Update debian-based packaging rules | 12 June 2023, 09:34:31 UTC |
| 1f51e92 | Ronny Lorenz | 11 June 2023, 22:33:37 UTC | AUTOCONF: Update openmp and python interface macros | 12 June 2023, 09:32:06 UTC |
| a20026e | Ronny Lorenz | 11 June 2023, 22:33:08 UTC | AUTOCONF: Update autoconf macros | 12 June 2023, 09:32:02 UTC |
| eefeead | Ronny Lorenz | 11 June 2023, 21:36:28 UTC | AUTOTOOLS: Rename AM conditionals for gengetopt and help2man | 12 June 2023, 09:32:02 UTC |
| e23483c | Ronny Lorenz | 11 June 2023, 21:33:50 UTC | AUTOTOOLS: Change check for OpenMP and allow for deactivation | 12 June 2023, 09:32:02 UTC |
| 7f31c9c | Marco Matthies | 11 June 2023, 11:36:38 UTC | Fix compilation on linux-musl Compiles fine for linux-glibc, macos, windows-mingw32, freebsd. Ref: https://github.com/JuliaPackaging/Yggdrasil/pull/6869 | 12 June 2023, 09:32:02 UTC |
| 5565031 | Ronny Lorenz | 11 June 2023, 11:05:09 UTC | Fix RNAdos double free and input sequence checks | 11 June 2023, 11:05:09 UTC |
| 75241dd | Ronny Lorenz | 07 June 2023, 06:08:46 UTC | Update CHANGELOG.md | 09 June 2023, 18:49:56 UTC |
| 46e5c6c | Ronny Lorenz | 02 June 2023, 19:05:18 UTC | Set up github release action workflow | 09 June 2023, 18:49:56 UTC |
| d27ad43 | Ronny Lorenz | 02 June 2023, 17:57:37 UTC | Test github workflow pre-release | 09 June 2023, 18:49:56 UTC |
| bf369f7 | Ronny Lorenz | 02 June 2023, 14:00:08 UTC | Update packaging/debian | 09 June 2023, 18:49:56 UTC |
| 67ef275 | Ronny Lorenz | 02 June 2023, 13:59:43 UTC | Update packaging/viennarna.spec | 09 June 2023, 18:49:56 UTC |
| 8575951 | Ronny Lorenz | 02 June 2023, 08:42:10 UTC | SWIG: Deactivate Python 2 bindings by default | 09 June 2023, 18:49:56 UTC |
| fcb8659 | Ronny Lorenz | 02 June 2023, 08:32:40 UTC | Prepare for release v2.6.0 | 09 June 2023, 18:49:56 UTC |
| f4581e2 | Ronny Lorenz | 09 June 2023, 14:55:49 UTC | SWIG: Add all RNAxplorer swig module dependencies to automake | 09 June 2023, 18:49:56 UTC |
| a5b4827 | Ronny Lorenz | 02 June 2023, 08:48:33 UTC | DOC: Update date string in doxygen main file | 09 June 2023, 18:49:56 UTC |
| 0577ed8 | Ronny Lorenz | 09 June 2023, 11:01:54 UTC | DOC: Fix doxygen comments on vrna_file_fasta_read_record() | 09 June 2023, 18:49:56 UTC |
| f76b8a9 | Ronny Lorenz | 09 June 2023, 18:49:49 UTC | SWIG: Restore backward compatibility with concensus/consens_mis functions | 09 June 2023, 18:49:49 UTC |
| 428771e | Ronny Lorenz | 08 June 2023, 20:18:49 UTC | SWIG: Add examples to pydoc | 08 June 2023, 20:18:49 UTC |
| e5d26f5 | Ronny Lorenz | 08 June 2023, 20:17:54 UTC | SWIG: Fix circular dependency in pydoc automake rules | 08 June 2023, 20:17:54 UTC |
| 9dcebe8 | Ronny Lorenz | 08 June 2023, 20:17:40 UTC | SWIG: Fix how doxy2swig produces notes section headings | 08 June 2023, 20:17:40 UTC |
| 3e9ac32 | Ronny Lorenz | 08 June 2023, 13:46:12 UTC | SWIG: Minor changes/fixes in duplex wrapper and consensus sequences | 08 June 2023, 13:46:12 UTC |
| d6427cc | Ronny Lorenz | 08 June 2023, 13:45:12 UTC | SWIG: Add and use ignore_list.csv for Python docstring corrections | 08 June 2023, 13:45:12 UTC |
| 88b621a | Ronny Lorenz | 08 June 2023, 13:41:46 UTC | SWIG: Add ignore/replace list and allow #define in doxy2swig | 08 June 2023, 13:41:46 UTC |
| 2aca984 | Ronny Lorenz | 08 June 2023, 07:50:09 UTC | SWIG: Fix double occurrence of return value in file_connect_read_record | 08 June 2023, 07:50:09 UTC |
| 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 |
