| 4a0e008 | Ronny Lorenz | 25 September 2023, 18:08:42 UTC | AUTOCONF: Use soft-check for fotran compiler and lapacke.h to test RNAxplorer build capabilities | 25 September 2023, 18:08:42 UTC |
| 20e0a8a | Ronny Lorenz | 25 September 2023, 11:28:37 UTC | WORKFLOWS: Fix ubuntu build dependencies for dist tarballs | 25 September 2023, 14:11:45 UTC |
| 48c5f28 | Ronny Lorenz | 25 September 2023, 11:28:37 UTC | DOC: Fix images in reference manual to build with older sphinx/convert | 25 September 2023, 14:10:09 UTC |
| 2fde6e8 | Ronny Lorenz | 25 September 2023, 09:15:43 UTC | SWIG: Define SWIGPY_SLICEOBJECT if not already defined by swig | 25 September 2023, 09:15:43 UTC |
| 1d906a4 | Ronny Lorenz | 22 September 2023, 10:29:43 UTC | Prepare for release of v2.6.4 | 25 September 2023, 08:38:28 UTC |
| 6ec4ba4 | Ronny Lorenz | 23 September 2023, 12:49:12 UTC | AUTOCONF: Fix check for pre-build reference manual | 23 September 2023, 12:50:51 UTC |
| 2098fbd | Ronny Lorenz | 22 September 2023, 19:43:13 UTC | DOC: Include man2rst.py and do not install .rst manpages | 22 September 2023, 19:58:54 UTC |
| 2d0b4d6 | Ronny Lorenz | 22 September 2023, 19:42:27 UTC | SWIG: Remove unused swig flags for Python 3 interface | 22 September 2023, 19:58:53 UTC |
| 80b0737 | Ronny Lorenz | 22 September 2023, 16:06:26 UTC | SWIG: Make inverse.i compile for Python 2 again | 22 September 2023, 19:58:49 UTC |
| 0ca2ad9 | Ronny Lorenz | 22 September 2023, 19:41:02 UTC | SWIG: Make var_arrays.i compile for Python 2 again | 22 September 2023, 19:58:42 UTC |
| 99da301 | Ronny Lorenz | 20 September 2023, 07:57:06 UTC | SWIG: Try circumvent bogus delete/free calls in swig interface | 22 September 2023, 07:48:14 UTC |
| 617bf2a | Ronny Lorenz | 18 September 2023, 18:49:17 UTC | WORKFLOWS: Enable build of Python interface for Linux Arm64 | 21 September 2023, 12:58:46 UTC |
| 833c45f | Ronny Lorenz | 18 September 2023, 18:49:17 UTC | SWIG: Disable SIMD implementations when building for arm via setup.py | 20 September 2023, 14:29:18 UTC |
| ea5b1d2 | Ronny Lorenz | 17 September 2023, 14:44:46 UTC | DOC: Move all citations to sphinx This patch moves all remaining citations from doxygen into the sphinx .rst realm. It also introduces a 'Citation' section in the reference documentation such that users can easily look-up what to cite if they use our software. Moreover, all references are equipped with a doi now, if available. | 17 September 2023, 14:44:51 UTC |
| 2ac6e0c | Ronny Lorenz | 16 September 2023, 09:38:44 UTC | Fix RNAsubopt backtracing error for duplexes with modified bases | 16 September 2023, 10:26:13 UTC |
| d916ac0 | Ronny Lorenz | 13 September 2023, 09:35:09 UTC | DOC: Minor cleanup in reference manual | 13 September 2023, 09:35:09 UTC |
| f0e7274 | Ronny Lorenz | 13 September 2023, 09:34:41 UTC | WORKFLOWS: update Ubuntu packages required to build reference manual | 13 September 2023, 09:34:41 UTC |
| d6f985f | Ronny Lorenz | 12 September 2023, 12:16:00 UTC | DOC: small changes for barriers/treekin tutorial | 12 September 2023, 12:16:00 UTC |
| 5e6a3d6 | Ronny Lorenz | 12 September 2023, 07:33:18 UTC | DOC: Change manpages inclusion and add tutorials to reference manual | 12 September 2023, 10:21:45 UTC |
| 5dbeb65 | Ronny Lorenz | 04 September 2023, 21:41:08 UTC | Update autoconf macros for blas and lapack | 04 September 2023, 21:41:08 UTC |
| 5ee08a5 | Ronny Lorenz | 04 September 2023, 21:40:30 UTC | Update configure.ac | 04 September 2023, 21:40:30 UTC |
| 40d5fb5 | Ronny Lorenz | 04 September 2023, 21:38:56 UTC | AUTOCONF: Deactivate RNAxplorer build if lapack is missing | 04 September 2023, 21:38:56 UTC |
| 396a7d8 | Ronny Lorenz | 04 September 2023, 09:26:19 UTC | SWIG: Remove 'embed:rst tags from verbatim parts in python docstrings | 04 September 2023, 09:26:19 UTC |
| 4618d83 | Ronny Lorenz | 04 September 2023, 08:08:41 UTC | DOC: Tidy-up --help and manpage documentation for --pfScale option in RNApvmin | 04 September 2023, 08:14:37 UTC |
| 1e26f89 | Ronny Lorenz | 04 September 2023, 07:55:42 UTC | DOC: Refactor autoconf checks for capability to build reference manual | 04 September 2023, 08:14:33 UTC |
| 9f6c894 | Ronny Lorenz | 04 September 2023, 07:55:10 UTC | SWIG: Return var_array<vrna_move_t> objects in Python wrapped vrna_neighbors() and vrna_move_neighbor_diff() | 04 September 2023, 08:14:32 UTC |
| 8fe4f16 | Ronny Lorenz | 04 September 2023, 07:53:59 UTC | SWIG: Add var_array<vrna_move_t> wrapper to effectively shadow arrays of type vrna_move_t | 04 September 2023, 08:14:32 UTC |
| 4093b7a | Ronny Lorenz | 04 September 2023, 07:52:36 UTC | SWIG: Add class output parameter typemap for Python | 04 September 2023, 08:14:19 UTC |
| 858f79f | Ronny Lorenz | 01 September 2023, 12:13:15 UTC | Fix potential NULL pointer dereferencing in BT_fms5_split() of mfe.c | 01 September 2023, 12:13:15 UTC |
| 38bcf08 | Ronny Lorenz | 01 September 2023, 12:12:42 UTC | Simplify Newton_Conc() in concentrations.c | 01 September 2023, 12:12:42 UTC |
| 13e17ea | Ronny Lorenz | 01 September 2023, 12:12:11 UTC | Fix potential use of uninitialized variable in vrna_rotational_symmetry_db_pos() | 01 September 2023, 12:12:11 UTC |
| 077960e | Ronny Lorenz | 01 September 2023, 12:11:17 UTC | Fix potentialy leaking memory in rnaplot_EPS() of plotting/structures.c | 01 September 2023, 12:11:17 UTC |
| 3b52f41 | Ronny Lorenz | 01 September 2023, 12:10:33 UTC | Fix potentially leaking file pointer in vrna_file_msa_read() | 01 September 2023, 12:10:33 UTC |
| 824d5e0 | Ronny Lorenz | 01 September 2023, 10:04:33 UTC | TESTS: Deactivate all non-redundant Boltzmann sampling tests on Windows | 01 September 2023, 10:04:33 UTC |
| aaa7d71 | Ronny Lorenz | 31 August 2023, 19:23:12 UTC | DOC: adapt autoconf requirements check for reference manual and python docstrings | 01 September 2023, 10:00:04 UTC |
| 3f2a3b4 | Ronny Lorenz | 01 September 2023, 08:19:34 UTC | WORKFLOWS: Add sphinx-build and requirements for dist build | 01 September 2023, 10:00:04 UTC |
| 2c41914 | Ronny Lorenz | 01 September 2023, 08:18:08 UTC | WORKFLOWS: Add windows python packages for PyPI build and adapt for Sphinx reference manual | 01 September 2023, 10:00:04 UTC |
| f4d8039 | Ronny Lorenz | 31 August 2023, 22:09:41 UTC | TESTS: Skip non-redundant Boltzmann sampling resume on Windows platform | 01 September 2023, 10:00:04 UTC |
| 9b5327d | Ronny Lorenz | 31 August 2023, 22:05:13 UTC | TESTS: fix tests for enumerate_necklaces() if sequences are shifted | 01 September 2023, 10:00:04 UTC |
| 2ec875a | Ronny Lorenz | 31 August 2023, 21:29:32 UTC | TESTS: Add conftest.py to tests/python/ directory for use with pytest | 01 September 2023, 10:00:04 UTC |
| 42c1a14 | Ronny Lorenz | 31 August 2023, 14:58:26 UTC | TESTS: Make tests run on Windows | 01 September 2023, 09:56:57 UTC |
| 03ba51e | Ronny Lorenz | 01 September 2023, 08:20:12 UTC | AUTOCONF: Add VRNA_VERSION to CPP defines | 01 September 2023, 09:56:57 UTC |
| 7a3036e | Ronny Lorenz | 30 August 2023, 11:25:00 UTC | SWIG: Adapt setup.py for windows build | 01 September 2023, 09:56:57 UTC |
| 91965e8 | Ronny Lorenz | 31 August 2023, 14:59:02 UTC | Use specific msvc cpuid query call in windows | 01 September 2023, 09:56:57 UTC |
| 35c1155 | Ronny Lorenz | 30 August 2023, 22:08:58 UTC | Redefined S_ISDIR() macro for windows builds | 01 September 2023, 09:56:57 UTC |
| bdd453a | Ronny Lorenz | 30 August 2023, 21:43:20 UTC | Use strtok_s() instead if strtok_r for windows builds | 01 September 2023, 09:56:57 UTC |
| b4033b0 | Ronny Lorenz | 30 August 2023, 12:52:02 UTC | Remove UNUSED from subopt.c | 01 September 2023, 08:38:51 UTC |
| d5cb276 | Ronny Lorenz | 30 August 2023, 12:15:20 UTC | Fix char array init in snoop.c | 01 September 2023, 08:38:51 UTC |
| 441a20b | Ronny Lorenz | 30 August 2023, 12:03:50 UTC | Remove unused troublesome code in RNApuzzler | 01 September 2023, 08:38:51 UTC |
| 9830cb6 | Ronny Lorenz | 30 August 2023, 11:40:05 UTC | Remove unnecessary header file libgen.h from io/io_utils.h | 01 September 2023, 08:38:51 UTC |
| d5b7825 | Ronny Lorenz | 30 August 2023, 10:59:58 UTC | remove inline assembler in vrna_C11_features() | 01 September 2023, 08:38:51 UTC |
| 67c759e | Ronny Lorenz | 30 August 2023, 10:36:47 UTC | SWIG: Fix signed/unsigned comparison in var_arrays.i | 01 September 2023, 08:38:51 UTC |
| 2122d79 | Ronny Lorenz | 30 August 2023, 10:20:32 UTC | SWIG: remove use of fcntl in file_py3.i | 01 September 2023, 08:38:51 UTC |
| afa6a92 | Ronny Lorenz | 30 August 2023, 08:27:20 UTC | Add unistd.h repacement for windows builds | 01 September 2023, 08:38:45 UTC |
| 65ac791 | Ronny Lorenz | 29 August 2023, 18:39:00 UTC | (Hopefully) last index fixes for vrna_move_neighbor_diff_cb() | 29 August 2023, 18:39:00 UTC |
| 3172054 | Ronny Lorenz | 29 August 2023, 08:36:25 UTC | More code cleanup in vrna_move_neighbor_diff_cb() | 29 August 2023, 08:36:25 UTC |
| 746bc13 | Ronny Lorenz | 28 August 2023, 22:51:34 UTC | Even more cleanup in vrna_move_neighbor_diff_cb() | 28 August 2023, 22:51:34 UTC |
| ef5a81e | Ronny Lorenz | 28 August 2023, 13:33:37 UTC | More simplifications in vrna_move_neighbor_diff_cb() | 28 August 2023, 13:33:37 UTC |
| ee0ba7d | Ronny Lorenz | 28 August 2023, 11:12:19 UTC | Revisit shift moves in vrna_move_neighbor_diff_cb() - This also implements the missing changed shift moves when a shift move has been applied. Also, it introduces some preprocessor macros to reduce the amount of written code and to prevent accidental mistakes... | 28 August 2023, 11:12:47 UTC |
| b6f85a0 | Ronny Lorenz | 25 August 2023, 20:11:34 UTC | SWIG: Add __hash__ and __eq__ methods for wrapped vrna_move_t in Python This allows for using set() operations on collections of moves. | 25 August 2023, 20:11:39 UTC |
| 9f51105 | Ronny Lorenz | 25 August 2023, 20:10:49 UTC | Fix and add still missing parts for shift moves in vrna_move_diff_cb() | 25 August 2023, 20:10:49 UTC |
| b83eaa5 | Ronny Lorenz | 24 August 2023, 17:36:07 UTC | Seems like shift move support implementation is finished in vrna_move_neighbor_diff_cb() | 24 August 2023, 22:39:47 UTC |
| 07b1684 | Ronny Lorenz | 23 August 2023, 19:17:56 UTC | Finalize Shift move support for indicating invalid moves in vrna_move_neighbor_diff_cb() | 24 August 2023, 22:39:47 UTC |
| 2ce7033 | Ronny Lorenz | 14 April 2023, 11:48:35 UTC | CLEANUP: Uncrustify landscape/neighbor.[c,h] and landscape/local_neighbors.* | 24 August 2023, 22:39:47 UTC |
| ebd1f51 | Ronny Lorenz | 25 April 2022, 16:50:47 UTC | Start adding shift move support for new and updated neighbors | 24 August 2023, 22:39:47 UTC |
| fb97277 | Ronny Lorenz | 06 April 2022, 06:23:33 UTC | Fix previous commit for vrna_move_neighbor_diff_cb() draft | 24 August 2023, 22:39:47 UTC |
| ebec6bf | Ronny Lorenz | 01 April 2022, 17:13:52 UTC | Add draft for shift-move support in vrna_move_neighbor_diff_cb() This patch adds shift move support for invalidation of incompatible moves after application of the next via VRNA_NEIGHBOR_INVALID identifier. | 24 August 2023, 22:39:47 UTC |
| 095f73f | Ronny Lorenz | 24 August 2023, 22:22:45 UTC | Make color make portable and turn off colors on stdout redirect | 24 August 2023, 22:36:31 UTC |
| d71c87f | Ronny Lorenz | 24 August 2023, 10:36:19 UTC | Move silent rules for automake to separate file and introduce colors | 24 August 2023, 10:36:19 UTC |
| d1cbb64 | Ronny Lorenz | 23 August 2023, 10:09:02 UTC | Merge branch 'user-contrib' into development | 23 August 2023, 10:09:02 UTC |
| 6e2c427 | Ronny Lorenz | 23 August 2023, 08:41:24 UTC | Merge pull request #199 from fncnt/hardcode-json-support Always set VRNA_WITH_JSON_SUPPORT in vrna_config.h | 23 August 2023, 08:41:24 UTC |
| de627ad | Ronny Lorenz | 23 August 2023, 08:03:16 UTC | SWIG: Fix var_array Python slices and associated memory leak | 23 August 2023, 08:03:16 UTC |
| 7a7f949 | Ronny Lorenz | 22 August 2023, 20:51:30 UTC | DOC: Add note on required tools to build the reference manual | 22 August 2023, 20:51:30 UTC |
| e2b0441 | Ronny Lorenz | 22 August 2023, 20:51:02 UTC | DOC: Remove 'edit on github' link at readthedocs.org | 22 August 2023, 20:51:02 UTC |
| f2d227f | Ronny Lorenz | 22 August 2023, 20:01:34 UTC | DOC: Add FAQ entry for LTO errors while linking against RNAlib | 22 August 2023, 20:01:34 UTC |
| 481c304 | Ronny Lorenz | 22 August 2023, 18:53:36 UTC | DOC: Remove links to viennarna-python.readthedocs.io - We include the Python API description in the main reference manual now, so we start the deprecation process for the separate Python documentation website... | 22 August 2023, 18:53:38 UTC |
| eadde6a | Ronny Lorenz | 22 August 2023, 18:45:15 UTC | Fix 'make distcheck' after including manpages in sphinx refdoc | 22 August 2023, 18:45:15 UTC |
| 5a79178 | Ronny Lorenz | 21 August 2023, 22:20:56 UTC | DOC: change .readthedocs.yaml to publish full documentation - Here, we use sphinx-mutiproject to enable build of both, the reference manual as well as the Python documentation. | 22 August 2023, 12:09:43 UTC |
| 3954e0a | Ronny Lorenz | 22 August 2023, 07:26:25 UTC | DOC: Print sphinx log upon build errors | 22 August 2023, 12:01:13 UTC |
| 9fab04f | Ronny Lorenz | 22 August 2023, 07:24:20 UTC | DOC: Remove Python documentation from regular build and distribution - We include the Python documentation as part of the full reference manual now, so we don't need to build it seperately. But we keep the sources for now in doc/python such that we can still publish the documentation at viennarna-python.readthedocs.io. | 22 August 2023, 12:00:18 UTC |
| 2f25ed8 | Ronny Lorenz | 21 August 2023, 21:38:48 UTC | DOC: Tidy-up manpages for better conversion with help2man and man2rst | 21 August 2023, 21:38:48 UTC |
| 659a03f | Ronny Lorenz | 21 August 2023, 09:13:28 UTC | DOC: Fix breathe compatibility with Sphinx 7.2 | 21 August 2023, 21:36:13 UTC |
| da07721 | Ronny Lorenz | 21 August 2023, 09:08:00 UTC | DOC: Refactor doc/man2rst.py | 21 August 2023, 21:36:08 UTC |
| 04983e3 | Ronny Lorenz | 29 July 2023, 12:32:13 UTC | DOC: Fixup doxygen.conf | 21 August 2023, 09:34:36 UTC |
| a80d72c | Ronny Lorenz | 29 July 2023, 12:31:54 UTC | DOC: Add autogenerated man pages for the executable programs in reference manual | 21 August 2023, 09:34:36 UTC |
| 8451372 | Ronny Lorenz | 24 July 2023, 18:26:45 UTC | DOC: Make sure documentation can be build upon 'make dist' and alike | 21 August 2023, 09:34:36 UTC |
| fed06f9 | Ronny Lorenz | 24 July 2023, 18:26:11 UTC | SWIG: Fix error in cleanup of __pycache__ dirs | 21 August 2023, 09:34:36 UTC |
| 143660b | Ronny Lorenz | 24 July 2023, 18:25:31 UTC | DOC: Fix distclean and maintainer-clean rules in doc/ | 21 August 2023, 09:34:36 UTC |
| ca2228a | Ronny Lorenz | 24 July 2023, 12:21:34 UTC | DOC: xref remaining doxygen comments on swig wrapped functions | 21 August 2023, 09:34:36 UTC |
| b8c3eb7 | Ronny Lorenz | 24 July 2023, 11:21:11 UTC | DOC: More xref from main documentation to Python | 21 August 2023, 09:34:36 UTC |
| d5b7375 | Ronny Lorenz | 24 July 2023, 09:02:17 UTC | DOC: Fix wrong doxygen xml output with inline .rst | 21 August 2023, 09:34:36 UTC |
| 2ced745 | Ronny Lorenz | 24 July 2023, 07:50:02 UTC | DOC: use grep -E instead of egrep to build PDF reference manual | 21 August 2023, 09:34:23 UTC |
| 6f6e85b | Ronny Lorenz | 24 July 2023, 07:36:51 UTC | DOC: Start using (inline) .rst code in doxygen comments to create hyperrefs to Python API | 21 August 2023, 09:34:23 UTC |
| a1b8d93 | Ronny Lorenz | 24 July 2023, 07:35:41 UTC | DOC: Add shipped breathe extension to PYTHONPATH for sphinx | 21 August 2023, 09:34:23 UTC |
| 7c1f95a | Ronny Lorenz | 21 August 2023, 09:33:46 UTC | Merge commit '33ac7482804bd6a870db06813a68bc87dccc4811' as 'doc/breathe' | 21 August 2023, 09:33:46 UTC |
| 33ac748 | Ronny Lorenz | 21 August 2023, 09:33:46 UTC | Squashed 'doc/breathe/' content from commit edd2f96f git-subtree-dir: doc/breathe git-subtree-split: edd2f96fe07cec868e8a4a405a3263fcb4b68c7a | 21 August 2023, 09:33:46 UTC |
| dae7268 | Ronny Lorenz | 23 July 2023, 15:40:40 UTC | DOC: Fix some remaining remnants of the doxygen documentation | 21 August 2023, 09:30:10 UTC |
| 059a825 | Ronny Lorenz | 23 July 2023, 08:39:30 UTC | DOC: more reference manual html style formatting | 21 August 2023, 09:30:10 UTC |
| abe4c3e | Ronny Lorenz | 23 July 2023, 00:59:12 UTC | DOC: fix some remaining parts of the sphinx documentation | 21 August 2023, 09:30:10 UTC |
| 4319960 | Ronny Lorenz | 22 July 2023, 23:41:20 UTC | DOC: Make html manual nicer | 21 August 2023, 09:30:10 UTC |
