| eb8f860 | Ronny Lorenz | 20 July 2023, 08:04:22 UTC | Workflows: Fix typo in workflow calls | 20 July 2023, 08:04:22 UTC |
| 4dea3b3 | Ronny Lorenz | 19 July 2023, 18:01:29 UTC | Prepare for release of ViennaRNA Package 2.6.3 | 20 July 2023, 06:43:24 UTC |
| 7c45418 | Ronny Lorenz | 20 July 2023, 06:43:17 UTC | Add pythons ViennaRNA/ package to .spec filefor RPM builds | 20 July 2023, 06:43:17 UTC |
| ad411c3 | Ronny Lorenz | 20 July 2023, 06:40:34 UTC | SWIG: Fix make intructions for python interface | 20 July 2023, 06:40:34 UTC |
| 362516e | Ronny Lorenz | 12 July 2023, 18:17:50 UTC | Workflows: Publish to PyPI only on release or manual trigger | 12 July 2023, 19:59:08 UTC |
| a9384f2 | Ronny Lorenz | 12 July 2023, 18:04:35 UTC | Reformat README.md to move links to the end of document | 12 July 2023, 19:59:08 UTC |
| 935b2e6 | Ronny Lorenz | 12 July 2023, 12:40:00 UTC | Workflows: Enable upload of Python packages to PyPI | 12 July 2023, 19:59:08 UTC |
| 96e8f58 | Ronny Lorenz | 11 July 2023, 20:23:20 UTC | Workflows: Enable upload of Python packages to test.pypi.org | 12 July 2023, 19:59:08 UTC |
| e359ed9 | Ronny Lorenz | 11 July 2023, 18:08:42 UTC | Update README.md for separate Python package installation | 12 July 2023, 19:59:08 UTC |
| 83ab1f6 | Ronny Lorenz | 11 July 2023, 18:08:18 UTC | SWIG: Add missing meta data to pyproject.toml and setup.py | 12 July 2023, 19:59:08 UTC |
| 526a930 | Ronny Lorenz | 11 July 2023, 11:08:06 UTC | Workflows: Building OS X arm64 wheels | 12 July 2023, 19:59:08 UTC |
| c0b5277 | Ronny Lorenz | 10 July 2023, 12:20:29 UTC | Workflows: Add github workflow to build Python wheels | 12 July 2023, 19:59:08 UTC |
| 65398ff | Ronny Lorenz | 10 July 2023, 11:08:06 UTC | SWIG: Include all files for source tarball and update README.md | 12 July 2023, 19:59:08 UTC |
| 64450ad | Ronny Lorenz | 29 June 2023, 08:36:51 UTC | SWIG: enable the use of setuptools to build Python interface | 12 July 2023, 19:59:08 UTC |
| 3a99cea | Ronny Lorenz | 12 July 2023, 18:40:50 UTC | Workflows: Add more workflows and reuse them | 12 July 2023, 19:59:03 UTC |
| 51e950d | Ronny Lorenz | 12 July 2023, 18:39:30 UTC | Remove unused statements in loops/internal.[c,h] Those were reported by W. B. Langdon | 12 July 2023, 19:06:09 UTC |
| 3b7ed16 | Ronny Lorenz | 12 July 2023, 12:37:14 UTC | TESTS: Fix import problems for Python tests | 12 July 2023, 19:06:09 UTC |
| 3d9a03f | Ronny Lorenz | 10 July 2023, 19:51:29 UTC | TESTS: Fix bpp computation issue in python/test_RNA.py For some reason it seems that the global deprecated variable 'do_backtrack' is uninitialized (or 0) when calling pf_fold(). As a consequence, no base pair probabilities are computed and subsequent tests on the global pr matrix fail. | 12 July 2023, 19:06:09 UTC |
| 18fc465 | Ronny Lorenz | 10 July 2023, 18:35:03 UTC | TESTS: Read data dir from environment variable if not run as __main__ in python tests | 12 July 2023, 19:06:09 UTC |
| 35aeacc | Ronny Lorenz | 10 July 2023, 17:04:19 UTC | TESTS: Move import RNApath to __main__ in python tests | 12 July 2023, 19:06:09 UTC |
| a5b6389 | Ronny Lorenz | 10 July 2023, 10:14:40 UTC | Update CHANGELOG.md | 12 July 2023, 19:06:09 UTC |
| 494ad2a | Ronny Lorenz | 10 July 2023, 10:14:13 UTC | DOC: Update README.md | 12 July 2023, 19:06:09 UTC |
| 0a64941 | Ronny Lorenz | 09 July 2023, 12:36:01 UTC | TESTS: Change Python tests such that they can be run by pytest as well | 12 July 2023, 19:06:09 UTC |
| 34a1f02 | Ronny Lorenz | 10 July 2023, 08:44:07 UTC | Make src/json/ parser integral part of ViennaRNA Package | 12 July 2023, 19:06:02 UTC |
| 1defd44 | Ronny Lorenz | 07 July 2023, 16:22:52 UTC | Move modified base energy parameters into 'modified_base' object in JSON file(s) | 07 July 2023, 16:22:52 UTC |
| d5b6c58 | Ronny Lorenz | 28 June 2023, 09:22:27 UTC | Add enthalpies and terminal end parameters for dihydrouridine | 28 June 2023, 09:22:27 UTC |
| 1d6d28b | Ronny Lorenz | 21 June 2023, 09:40:48 UTC | Merge pull request #189 from marcom/fix-header-parse-size_t Fix missing include for size_t in constraints/soft.h | 21 June 2023, 09:40:48 UTC |
| dc3a071 | Ronny Lorenz | 21 June 2023, 09:05:30 UTC | Merge tag 'v2.6.2' into user-contrib This is release v2.6.2 | 21 June 2023, 09:05:30 UTC |
| dab2277 | Ronny Lorenz | 20 June 2023, 18:54:03 UTC | Prepare for release v2.6.2 | 20 June 2023, 23:24:26 UTC |
| 842b4d3 | Ronny Lorenz | 20 June 2023, 22:09:31 UTC | Adapt windows installer build scripts | 20 June 2023, 22:10:58 UTC |
| 4b1f13c | Ronny Lorenz | 20 June 2023, 16:35:51 UTC | Add ac_rxp_features.m4 | 20 June 2023, 16:35:51 UTC |
| f8232c2 | Ronny Lorenz | 20 June 2023, 16:02:18 UTC | SWIG: substitute C functions in Python docstring content with method calls if appropriate | 20 June 2023, 16:02:18 UTC |
| de7c6ae | Ronny Lorenz | 14 June 2023, 10:24:12 UTC | Use strstr() instead of strcasestr() in CT file parsing for compatibility reasons | 19 June 2023, 10:46:11 UTC |
| 3555678 | Marco Matthies | 19 June 2023, 08:16:26 UTC | Fix missing include for size_t, breaks parsing of header files | 19 June 2023, 08:16:26 UTC |
| e7333b6 | Ronny Lorenz | 18 June 2023, 22:12:23 UTC | Update CHANGELOG.md | 18 June 2023, 22:12:51 UTC |
| 3a102aa | Ronny Lorenz | 18 June 2023, 17:10:12 UTC | TESTS: Include duplex energy test for inosine | 18 June 2023, 22:06:51 UTC |
| 43b4863 | Ronny Lorenz | 16 June 2023, 23:07:48 UTC | TESTS: Include duplex energy test for pseudoridine | 18 June 2023, 22:06:51 UTC |
| 8da121f | Ronny Lorenz | 18 June 2023, 17:09:12 UTC | Add modified base parameters on pseudouridine duplexes | 18 June 2023, 22:06:51 UTC |
| 970ae91 | Ronny Lorenz | 18 June 2023, 17:08:49 UTC | Add modified base parameters on inosine duplexes with I-C pairs | 18 June 2023, 22:06:51 UTC |
| 47afe4b | Ronny Lorenz | 16 June 2023, 23:06:49 UTC | Add duplex data to pseudouridine data set | 18 June 2023, 22:06:51 UTC |
| 3ce8124 | Ronny Lorenz | 16 June 2023, 21:54:40 UTC | SWIG: Wrap energy parameter files as constant strings | 18 June 2023, 22:06:51 UTC |
| 800f362 | Ronny Lorenz | 15 June 2023, 20:18:55 UTC | Extend vrna_auxdata_prepare_f by an additonal argument The additional argument is a void * pointer that can serve as additional data passed from the library that may be helpful for any preparation. As a first case, we use this to distinguish between sliding-window and global structure prediction in constraints update callbacks. | 18 June 2023, 22:06:51 UTC |
| f498faf | Ronny Lorenz | 15 June 2023, 12:55:22 UTC | Store modified base positions on per-strand basis and refactor soft constraints multi callback implementation | 18 June 2023, 22:06:51 UTC |
| e72b144 | Ronny Lorenz | 14 June 2023, 21:45:41 UTC | Allow for soft constraints callback data to undergo preparation stage | 18 June 2023, 22:06:51 UTC |
| 706daa0 | Ronny Lorenz | 17 June 2023, 22:29:34 UTC | Add soft-constraints callback helpers to multifold pf implementation | 18 June 2023, 22:06:51 UTC |
| b442bbf | Ronny Lorenz | 17 June 2023, 21:35:30 UTC | Add soft-constraints callback helpers to multifold MFE implementation | 18 June 2023, 22:06:51 UTC |
| 86e57cb | Ronny Lorenz | 15 June 2023, 12:57:19 UTC | SWIG: Fix fc.sc_add_bp() propagation of constraint values | 18 June 2023, 22:05:22 UTC |
| ffbdaeb | Ronny Lorenz | 14 June 2023, 06:38:30 UTC | Update README.md | 14 June 2023, 06:38:30 UTC |
| 1be928f | Ronny Lorenz | 13 June 2023, 16:44:03 UTC | Update CHANGELOG.md | 13 June 2023, 16:49:29 UTC |
| 0b9354e | Ronny Lorenz | 13 June 2023, 16:33:17 UTC | Fix modified base implementation for cases where unmodified base != fallback | 13 June 2023, 16:49:29 UTC |
| 8c83dfe | Ronny Lorenz | 13 June 2023, 15:46:52 UTC | Fix modified_bases_helper.c sequence preparation for multiple input sequences | 13 June 2023, 16:49:24 UTC |
| e7eb42b | Ronny Lorenz | 12 June 2023, 12:22:32 UTC | Merge tag 'v2.6.1' into user-contrib This is version 2.6.1 | 12 June 2023, 12:22:32 UTC |
| 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 |
| cc5bc79 | Ronny Lorenz | 11 June 2023, 18:13:55 UTC | Merge pull request #187 from marcom/fix-musl Fix RNAxplorer compilation on linux-musl | 11 June 2023, 18:13:55 UTC |
| 2f6df0d | 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 | 11 June 2023, 11:36:38 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 |
