| 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 |
| ceb6a69 | Ronny Lorenz | 17 April 2023, 23:14:01 UTC | Fix memory leak in soft constraints modified base parser | 20 April 2023, 20:04:54 UTC |
| 59e1036 | Ronny Lorenz | 17 April 2023, 23:13:21 UTC | Fix memory leak in soft constraints multi callback implementation | 20 April 2023, 20:04:54 UTC |
| 63b8c45 | Ronny Lorenz | 20 April 2023, 20:02:20 UTC | SWIG: only accept upper-triangular part of matrix input in fc.sc_bp_add() method | 20 April 2023, 20:03:36 UTC |
| 231978d | Ronny Lorenz | 20 April 2023, 07:28:23 UTC | Fix soft constraints callback in Zuker subopt This fixes the missing application of soft constraints callbacks for multibranch loop stems in the backtrackign stage | 20 April 2023, 07:28:27 UTC |
| 435d006 | Ronny Lorenz | 19 April 2023, 15:12:04 UTC | Fix backtracking failure in Zuker subopt This fixes backtracking failures due to the removal of the min_loop_size checks in zuker subopt as introduced by commit b161f74a4f3f821096feb3de45a0c12d44560dd2 | 19 April 2023, 15:12:07 UTC |
| 36c2e68 | Ronny Lorenz | 05 April 2023, 18:24:59 UTC | Remove unused csv output functions in RNAmultifold | 05 April 2023, 20:23:35 UTC |
| 71db468 | Ronny Lorenz | 05 April 2023, 18:24:15 UTC | Fix CSV output in RNAcofold This fixes a bug in CSV header formatting of RNAcofold introduced by commit a110ba7 and release with version 2.4.7 | 05 April 2023, 20:22:46 UTC |
| b918db1 | Ronny Lorenz | 01 April 2023, 12:32:22 UTC | Fix default salt concentration Boltzmann factors for long hairpins and internal loops | 05 April 2023, 14:32:40 UTC |
| 373897f | Ronny Lorenz | 05 April 2023, 14:32:24 UTC | Merge remote-tracking branch 'origin/feature/salt' into development | 05 April 2023, 14:32:24 UTC |
| 4deaba4 | Ronny Lorenz | 02 April 2023, 11:41:55 UTC | Bump libsvm to version 3.31 | 05 April 2023, 14:31:48 UTC |
| 028dcee | Ronny Lorenz | 02 April 2023, 11:03:21 UTC | Remove RNAxplorer.1 manpage during distclean | 05 April 2023, 14:31:33 UTC |
| baa4fcb | Ronny Lorenz | 01 April 2023, 12:32:47 UTC | SWIG: Refactor RNAxplorer Python interface make rules | 05 April 2023, 14:31:20 UTC |
| 1b681f4 | Ronny Lorenz | 05 April 2023, 14:29:08 UTC | AUTOCONF: Fix configure check for libgsl when library is present and headers are missing | 05 April 2023, 14:29:40 UTC |
| b5a54d6 | Hua-Ting Yao | 03 March 2023, 13:34:34 UTC | Complete documentation | 03 March 2023, 13:34:34 UTC |
| 6b80ab1 | Hua-Ting Yao | 02 March 2023, 22:41:18 UTC | Complete cml tool, set saltInit as hidden argument | 02 March 2023, 22:41:18 UTC |
| fc11e76 | Hua-Ting Yao | 02 March 2023, 19:38:46 UTC | Merge two option for saltinit | 02 March 2023, 19:38:46 UTC |
| b3085fe | Hua-Ting Yao | 02 March 2023, 13:34:51 UTC | Include salt option in cmd tool | 02 March 2023, 13:34:51 UTC |
| 03d6ad8 | Hua-Ting Yao | 02 March 2023, 11:49:24 UTC | Set salt related parameter, and change fitted duplex init | 02 March 2023, 11:49:24 UTC |
| 65ecb8d | Hua-Ting Yao | 23 February 2023, 14:38:38 UTC | Add salt option to some cmd tool | 23 February 2023, 14:38:38 UTC |
| d79be69 | Hua-Ting Yao | 22 February 2023, 20:34:39 UTC | Add correction for loop >30 and alignment | 22 February 2023, 20:34:39 UTC |
| 5717f78 | Hua-Ting Yao | 22 February 2023, 14:07:14 UTC | Remove model option for stadard concentration | 22 February 2023, 14:07:14 UTC |
| 4dcebb1 | Hua-Ting Yao | 22 February 2023, 12:43:12 UTC | Use temperature dependent epsilon r | 22 February 2023, 12:43:12 UTC |
| 8be41d4 | Hua-Ting Yao | 16 February 2023, 10:51:25 UTC | Move salt files from loops/ to params/ | 16 February 2023, 10:51:25 UTC |
| e993c9f | Hua-Ting Yao | 30 January 2023, 15:35:59 UTC | Set standard salt concentration at 1.021M | 30 January 2023, 15:35:59 UTC |
| f0a46a4 | Hua-Ting Yao | 27 January 2023, 08:46:41 UTC | Add fitted duplex init | 27 January 2023, 08:46:41 UTC |
| ec840a2 | Hua-Ting Yao | 12 January 2023, 09:31:24 UTC | Add default salt linear param | 12 January 2023, 09:31:24 UTC |
| dfd3bd6 | Ronny Lorenz | 27 December 2022, 20:05:14 UTC | Merge branch 'dev_rnaxplorer' into development | 27 December 2022, 20:05:14 UTC |
| 826cbe7 | Ronny Lorenz | 27 December 2022, 19:38:46 UTC | SWIG: Fix Perl 5 wrapper for vrna_ud_prob_get() | 27 December 2022, 20:04:21 UTC |
| 1a07ef8 | Ronny Lorenz | 27 December 2022, 19:33:40 UTC | Merge remote-tracking branch 'github/user-contrib' into development | 27 December 2022, 19:33:40 UTC |
| c0b7378 | Ronny Lorenz | 27 December 2022, 19:33:12 UTC | Revert "Fix Python 3 build failure due to missing extension suffix" This reverts commit 1b976699f2c69d11ab94435b39e16e96faf1a6bf in favor of Michael Souzas commit submitted via github | 27 December 2022, 19:33:12 UTC |
| df835a9 | Ronny Lorenz | 27 December 2022, 19:29:27 UTC | Fix z-score init for vrna_Lfoldz() and vrna_mfe_window_zscore_cb() - This fixes an initialization issue for sliding window z-score MFE filtering when the provided vrna_fold_compound_t does not contain a pre-initialized z-score options container | 27 December 2022, 19:29:57 UTC |
| a34d14f | Ronny Lorenz | 13 December 2022, 08:48:02 UTC | Require C++17 compiler for DLIB build | 13 December 2022, 08:48:02 UTC |
| 90f1ab9 | Ronny Lorenz | 13 December 2022, 08:39:48 UTC | Merge pull request #172 from domonik/patch-1 Closes commands file after it is read | 13 December 2022, 08:39:48 UTC |
| df238b5 | Ronny Lorenz | 13 December 2022, 08:37:24 UTC | Merge pull request #174 from sumslogs/fix-remove-distutils Fix: distutils related build failure in python 3.11, removal in 3.12 | 13 December 2022, 08:37:24 UTC |
| c6fce52 | Michael Souza | 12 December 2022, 23:29:57 UTC | Fix: distutils related build failure in python 3.11, removal in 3.12 distutils.sysconfig.get_config_var('SO') was deprecated in python 3.4, and is unset in python 3.11.0. Causes PYTHON3_SO=None -> _RNA.so builds as "_RNANone" -> build failure: ``` ImportError: cannot import name '_RNA' from partially initialized module 'RNA' ``` See: python/cpython#60958, python/cpython#63754 and [deprecation notice here](https://github.com/python/cpython/blob/dd53b79de0ea98af6a11481217a961daef4e9774/Doc/whatsnew/3.4.rst#deprecations-in-the-python-api). Also, module [distutils](https://docs.python.org/3/library/distutils.html) is deprecated and has planned removal in 3.12. Functions get_python_inc, get_python_lib are removed, see: python/cpython#92584. | 12 December 2022, 23:29:57 UTC |
| 1b97669 | Ronny Lorenz | 12 December 2022, 23:14:01 UTC | Fix Python 3 build failure due to missing extension suffix - distutils.sysconfig.get_config_vars('SO') has been deprecated for some time and apparently removed in Python 3.11. So we use the correct replacement distutils.sysconfig.get_config_vars('EXT_SUFFIX') instead | 12 December 2022, 23:14:03 UTC |
| 17123af | Dominik Rabsch | 30 November 2022, 13:03:51 UTC | Closes commands file after it is read closes commands file after it is read to avoid leaking open file descriptors | 30 November 2022, 13:03:51 UTC |
| 0ced3c1 | Ronny Lorenz | 22 October 2022, 12:59:09 UTC | Fix alignment input parsing in refold.pl | 22 October 2022, 12:59:09 UTC |
| 4fde5e6 | Hua-Ting Yao | 27 September 2022, 11:58:07 UTC | Integrate salt concentration correction term into params Start Salt correction Move all salt correction to params Adjust Multiloop related parameters for salt correction Salt correction for multiloop and exp function | 19 October 2022, 12:39:14 UTC |
| 20b2f48 | Ronny Lorenz | 18 October 2022, 20:44:17 UTC | Add RNAxplorer as subpackage | 18 October 2022, 20:44:17 UTC |
| aecac4c | Ronny Lorenz | 18 October 2022, 13:17:21 UTC | Merge commit '536ae07b38ac521addae44fc1c1668f31c99512f' as 'src/RNAxplorer' | 18 October 2022, 13:17:21 UTC |
| 536ae07 | Ronny Lorenz | 18 October 2022, 13:17:21 UTC | Squashed 'src/RNAxplorer/' content from commit 87226d19 git-subtree-dir: src/RNAxplorer git-subtree-split: 87226d19c89f54ba3dd69e0d6fe2d480b6916e71 | 18 October 2022, 13:17:21 UTC |
| 8384b0c | Ronny Lorenz | 18 October 2022, 12:35:54 UTC | Allow for at least as many threads as CPUs are configured - Sometimes, the sysconf() command returns an error, indicated by a return value of -1. As a consequence, the executable programs limit the maximum number of concurrent threads to 1. Now, we query the number of configured CPUs and take this value of maximum number of threads. This should work-around the issue for most systems where sysconf() doesn't work. | 18 October 2022, 12:35:57 UTC |
| 3d4fb1f | Hua-Ting Yao | 13 September 2022, 07:01:50 UTC | Salt correction for stack and simple loop | 13 September 2022, 07:01:50 UTC |
| 480c429 | Hua-Ting Yao | 09 September 2022, 22:54:21 UTC | Include minimum files from cephes library for kn function | 09 September 2022, 22:54:21 UTC |
| a815c66 | Hua-Ting Yao | 08 September 2022, 15:28:48 UTC | Add salt concentration parameter in model | 08 September 2022, 15:28:48 UTC |
| 364af14 | Ronny Lorenz | 01 September 2022, 12:37:34 UTC | CLEANUP: Uncrustify constraints/ligand.h | 01 September 2022, 12:37:34 UTC |
| 5f8f824 | Ronny Lorenz | 01 September 2022, 12:37:24 UTC | CLEANUP: Uncrustify constraints/SHAPE* | 01 September 2022, 12:37:24 UTC |
| c041d47 | Ronny Lorenz | 01 September 2022, 12:37:10 UTC | CLEANUP: Uncrustify constraints/basic.h | 01 September 2022, 12:37:10 UTC |
| e0be452 | Ronny Lorenz | 01 September 2022, 12:36:49 UTC | CLEANUP: Uncrustify constraints/sc_cb* | 01 September 2022, 12:36:49 UTC |
| 07e59f7 | Ronny Lorenz | 01 September 2022, 12:36:05 UTC | CLEANUP: Uncrustify constraints/hard* | 01 September 2022, 12:36:05 UTC |
| 9ca1e6b | Ronny Lorenz | 01 September 2022, 12:35:55 UTC | CLEANUP: Uncrustify constraints/soft* | 01 September 2022, 12:35:55 UTC |
| 82ec7ee | Ronny Lorenz | 30 July 2022, 23:18:33 UTC | Make function typedefs actual function pointer typedefs Previously, we mostly used function typedefs and pointer variables to refer to function pointers. This may be misleading and also results in doxygen to misbehave. So we transform all related typedefs into actual function pointers instead. This also introduces new names for all function pointers, where the new name always contains the suffix _f | 01 September 2022, 09:34:05 UTC |
| 0e49791 | Ronny Lorenz | 20 July 2022, 20:50:51 UTC | Fix some compile issues with RNAforester This fixes possible header include mixups and silences compiler warnings about wrong use of 'new' and 'delete' | 20 July 2022, 20:51:01 UTC |
| 98dd4bb | Ronny Lorenz | 15 July 2022, 08:39:05 UTC | Packaging: Adapt debian package dependencies | 15 July 2022, 08:39:05 UTC |
| fe5f501 | Ronny Lorenz | 15 July 2022, 08:38:26 UTC | AUTOCONF: Fix requirements check when SVM support is deactivated and swig is missing | 15 July 2022, 08:38:30 UTC |
| f921a00 | Ronny Lorenz | 08 July 2022, 20:44:12 UTC | DOC: Add documentation for modified base support via soft constraints callback mechanism | 08 July 2022, 20:45:20 UTC |
| a326530 | Ronny Lorenz | 08 July 2022, 20:42:52 UTC | SWIG: Add wrappers to construct vrna_sc_mod_param_t objects and use them in vrna_sc_mod() | 08 July 2022, 20:42:52 UTC |
| 15d653c | Ronny Lorenz | 08 July 2022, 20:41:47 UTC | Allow for NULL input for model_details in vrna_sc_mod_read_from_json*() | 08 July 2022, 20:41:47 UTC |
| a40e27b | Ronny Lorenz | 08 July 2022, 06:32:41 UTC | Rename modified base soft constraint callback mechanism for dihydrouridine | 08 July 2022, 06:59:08 UTC |
| 9cae23f | Ronny Lorenz | 08 July 2022, 06:28:14 UTC | Remove hard-coded soft constraints callback implementation for m6A | 08 July 2022, 06:59:04 UTC |
| 37eae53 | Ronny Lorenz | 08 July 2022, 06:27:41 UTC | Remove hard-coded soft constraints callback implementation for pseudouridine | 08 July 2022, 06:59:01 UTC |
| a107923 | Ronny Lorenz | 08 July 2022, 06:58:30 UTC | Remove hard-coded soft constraints callback implementation for inosine | 08 July 2022, 06:58:51 UTC |
| 8ac9e39 | Ronny Lorenz | 08 July 2022, 06:57:40 UTC | SWIG: Add wrappers for modified bases soft constraints mechanism | 08 July 2022, 06:57:40 UTC |
| 337ce1c | Ronny Lorenz | 08 July 2022, 06:23:33 UTC | Deactivate debugging output modified base in soft constraints framework | 08 July 2022, 06:23:33 UTC |
| 4b863f3 | Ronny Lorenz | 07 July 2022, 21:57:55 UTC | CLEANUP: Uncrustify constraints/soft_special.h | 07 July 2022, 21:57:55 UTC |
| 36f1714 | Ronny Lorenz | 07 July 2022, 21:57:30 UTC | CLEANUP: Uncrustify constraints/sc_cb_mod_wrappers.c | 07 July 2022, 21:57:30 UTC |
| 375b2e7 | Ronny Lorenz | 07 July 2022, 21:57:20 UTC | CLEANUP: Uncrustify constraints/sc_cb_mod_parser.c | 07 July 2022, 21:57:20 UTC |
| 33714d6 | Ronny Lorenz | 07 July 2022, 21:57:08 UTC | CLEANUP: Uncrustify constraints/sc_cb_mod.c | 07 July 2022, 21:57:08 UTC |
| 5597f8d | Ronny Lorenz | 07 July 2022, 21:35:51 UTC | Add convenience wrappers for compiled-in modified base soft constraints | 07 July 2022, 21:35:51 UTC |
| ea89f0d | Ronny Lorenz | 07 July 2022, 21:04:58 UTC | Prepare compiled JSON-formatted modified base energy parameters | 07 July 2022, 21:04:58 UTC |
| f24d8d8 | Ronny Lorenz | 07 July 2022, 21:04:22 UTC | Allow for separate modified bases soft constraints parameter retrieval and application | 07 July 2022, 21:04:22 UTC |
| 85a903b | Ronny Lorenz | 07 July 2022, 20:48:46 UTC | Split soft constraints callback mechanism for modified bases | 07 July 2022, 20:48:46 UTC |
| dd3feeb | Ronny Lorenz | 07 July 2022, 19:26:20 UTC | Distribute and install JSON parameter files for modified bases | 07 July 2022, 19:26:51 UTC |
| 31f2aad | Ronny Lorenz | 07 July 2022, 15:45:09 UTC | Add JSON parameter file for Purine (nebularine) | 07 July 2022, 19:26:51 UTC |
| bf413b6 | Ronny Lorenz | 07 July 2022, 15:44:51 UTC | Add JSON parameter file for Pseudouridine | 07 July 2022, 19:26:51 UTC |
| 5b40bec | Ronny Lorenz | 07 July 2022, 15:44:28 UTC | Add JSON parameter file for m6A | 07 July 2022, 19:26:51 UTC |
| f2e6038 | Ronny Lorenz | 07 July 2022, 15:44:14 UTC | Add JSON parameter file for Inosine | 07 July 2022, 19:26:51 UTC |
| 7ec48cc | Ronny Lorenz | 07 July 2022, 15:44:02 UTC | Add JSON parameter file for 7DA | 07 July 2022, 19:26:51 UTC |
| 2c2b631 | Ronny Lorenz | 07 July 2022, 17:53:40 UTC | Allow for non-canonical pairs in modified base soft constraint implementation | 07 July 2022, 19:26:51 UTC |
| 1705048 | Ronny Lorenz | 07 July 2022, 14:47:25 UTC | Add preliminary functions for arbitrary modified base support This is implemented via soft constraints callbacks while parameters and other meta-data is read from a JSON-formatted input file | 07 July 2022, 14:47:37 UTC |
| 43b9b2a | Ronny Lorenz | 07 July 2022, 14:45:41 UTC | Add preliminary implementation for string data structure | 07 July 2022, 14:45:41 UTC |
| d3b7205 | Ronny Lorenz | 07 July 2022, 14:44:27 UTC | SWIG: Add sc_inosine() method to fold_compound objects | 07 July 2022, 14:44:27 UTC |
| 1aa3829 | Ronny Lorenz | 07 July 2022, 14:43:26 UTC | Add I-C pairs to inosine soft constraints callbacks | 07 July 2022, 14:43:26 UTC |
| 28ca45a | Ronny Lorenz | 07 July 2022, 14:42:39 UTC | Fix temperature scaling in m6A-U soft constraints callbacks | 07 July 2022, 14:42:39 UTC |
| e3c6258 | Ronny Lorenz | 07 July 2022, 14:41:55 UTC | Fix temperature scaling in Psi-A soft constraints callbacks | 07 July 2022, 14:41:55 UTC |
| 084e340 | Ronny Lorenz | 30 June 2022, 10:18:54 UTC | Fix orientation of enclosed pairs for m6A-U and psi-A soft constraints callbacks - This adds dH and dG_37 values for the psi-A stacking and Terminal Psi-A parameters such that they can be rescaled to different temperatures. | 30 June 2022, 10:18:59 UTC |
| 49042da | Ronny Lorenz | 30 June 2022, 10:17:06 UTC | Add inosine-U parameter soft constraint callbacks | 30 June 2022, 10:17:29 UTC |
| e60a246 | Ronny Lorenz | 30 June 2022, 10:12:11 UTC | DOC: Reorder refman documentation for dynamic array implementation | 30 June 2022, 10:12:11 UTC |
| 8240299 | Ronny Lorenz | 30 June 2022, 10:11:06 UTC | Fix potential problems in free_dp_matrices() of LPfold.c | 30 June 2022, 10:11:06 UTC |
| acb6a6b | Ronny Lorenz | 30 June 2022, 10:10:02 UTC | Update dlib to version 19.24 | 30 June 2022, 10:10:02 UTC |
| ac67cac | Ronny Lorenz | 29 June 2022, 07:38:04 UTC | Refactor dynamic array implementation for the sake of simplicity | 29 June 2022, 07:38:04 UTC |
| 52d6413 | Ronny Lorenz | 27 June 2022, 21:42:06 UTC | SWIG: wrap m6A, Pseudouridine and dihydrouridine energy corrections | 27 June 2022, 21:46:28 UTC |
| 4b427a9 | Ronny Lorenz | 27 June 2022, 21:39:50 UTC | Add partition function variant for soft constraints multi callback wrapper - Also simplify the wrapper architecture and provide default partition function variant | 27 June 2022, 21:45:33 UTC |
| 6dc14fb | Ronny Lorenz | 27 June 2022, 19:54:27 UTC | Add Dihydrouridine stacking penalty soft constraints callback | 27 June 2022, 21:45:33 UTC |
| 9d56251 | Ronny Lorenz | 27 June 2022, 19:52:46 UTC | Add Pseudouridine-A stacking parameter adjustment callbacks | 27 June 2022, 21:45:33 UTC |
