| 8aad266 | Aidan Delaney | 25 June 2014, 21:21:05 UTC | Minor bump to account for dependency on fastml2, rather than fastml3. | 25 June 2014, 21:21:05 UTC |
| 4c79171 | Aidan Delaney | 25 June 2014, 21:19:42 UTC | Forced use of correct packaging key | 25 June 2014, 21:19:42 UTC |
| d997fa3 | Aidan Delaney | 23 April 2014, 13:21:11 UTC | Updated debain package compat to something modern | 23 April 2014, 13:21:11 UTC |
| e761ef4 | Aidan Delaney | 16 April 2014, 10:45:12 UTC | Made external dependancies test look for binaries in $PATH rather than the previously bundled versions. | 16 April 2014, 10:45:12 UTC |
| f01a4f6 | Aidan Delaney | 16 April 2014, 10:44:38 UTC | Changed tar format as some of our test files go over the "traditional" 99 char length. | 16 April 2014, 10:44:38 UTC |
| 5aa912d | Aidan Delaney | 08 April 2014, 13:19:14 UTC | Integrated gubbins python bindings tests into the build. | 08 April 2014, 13:19:14 UTC |
| 145ae49 | Aidan Delaney | 08 April 2014, 11:46:17 UTC | Having removed the source of the external dependencies, we modify the python bindings such that they no longer use them. | 08 April 2014, 11:46:17 UTC |
| a836206 | Aidan Delaney | 08 April 2014, 10:11:44 UTC | External source dependencies are removed as they are now all available as .deb packages. | 08 April 2014, 10:11:44 UTC |
| 2f65344 | Aidan Delaney | 08 April 2014, 10:00:35 UTC | All of our external dependencies are now provided as Ubuntu packages. - the RaXML build uses the Makefile.generic which is the same as what is used by the Debian/Ubuntu packages. - fastml is now packaged in PPA for Ubuntu saucy, we'll expand this coverage later. | 08 April 2014, 10:00:35 UTC |
| 0e88f50 | Aidan Delaney | 07 April 2014, 12:42:20 UTC | Merge pull request #1 from zamaudio/deb_tweaks Made RaXML a recommended package, not a dependency, | 07 April 2014, 12:42:20 UTC |
| 4110d4d | Damien Zammit | 06 April 2014, 13:01:06 UTC | Made RaXML a recommended package, not a dependency, since standard-raxml will be built if it is not found. Also, some HPC facilities have customised builds of RaXML so it is not ideal to make the binary package a strict dependency. | 06 April 2014, 13:06:06 UTC |
| 6392f5d | Aidan Delaney | 01 April 2014, 10:35:29 UTC | Updated package dependancy list to include some of the python deps. | 01 April 2014, 10:35:29 UTC |
| 174d202 | Aidan Delaney | 31 March 2014, 19:26:53 UTC | Streamlining the Debiab/Ubuntu package release - Use @PACKAGE_*@ autoconf vars - generate some debian/* files | 31 March 2014, 19:26:53 UTC |
| 394eea2 | Aidan Delaney | 30 March 2014, 15:04:40 UTC | Added setup.py to the make | 30 March 2014, 15:04:40 UTC |
| 3c78f5a | Aidan Delaney | 25 March 2014, 07:14:06 UTC | Updated Debian build number to unclude a PPA string. | 25 March 2014, 07:14:06 UTC |
| 7b5ab17 | Aidan Delaney | 23 March 2014, 21:02:25 UTC | Use cp to /vagrant rather than scp - SCP likes to check the host key of our temporay VM, and won't connect if it has seen localhost:2222 before (which it probably has). | 23 March 2014, 21:02:25 UTC |
| e4e354b | Aidan Delaney | 23 March 2014, 20:20:32 UTC | Copy the .changes, .dsc and possibly modified .tar.gz to the build host. | 23 March 2014, 20:20:32 UTC |
| 0cc4894 | Aidan Delaney | 23 March 2014, 19:29:02 UTC | Build and configuration changes needed to build a gubbins .deb package. | 23 March 2014, 19:29:02 UTC |
| b83b2d6 | Aidan Delaney | 23 March 2014, 18:36:13 UTC | Make -lrt explicit for the tests (for POSIX timers). | 23 March 2014, 18:36:13 UTC |
| 989930c | Aidan Delaney | 23 March 2014, 18:17:46 UTC | libgubbins depends on libm, not just the gubbins binary. | 23 March 2014, 18:17:46 UTC |
| 1e83197 | Aidan Delaney | 23 March 2014, 17:31:29 UTC | Added minimial number of control files for a valid Debian package. | 23 March 2014, 17:31:29 UTC |
| a6f6836 | Aidan Delaney | 23 March 2014, 17:20:08 UTC | Added initial plumbing to get a configured Ubuntu 13.10 VM for release builds. | 23 March 2014, 17:20:08 UTC |
| c752294 | Aidan Delaney | 22 March 2014, 20:54:10 UTC | Modified the README to point at the INSTALL file for build instructions. | 22 March 2014, 20:54:10 UTC |
| a732c83 | Aidan Delaney | 22 March 2014, 20:25:17 UTC | Removed more autogenerated files and updated build documentation. | 22 March 2014, 20:25:17 UTC |
| 86c872c | Aidan Delaney | 22 March 2014, 20:14:31 UTC | Removed some autogenerated files. | 22 March 2014, 20:14:31 UTC |
| 975dd5a | Aidan Delaney | 22 March 2014, 20:01:26 UTC | Removed the external dependencies from the build - these are deps of the Python wrapper, not libgubbins.so. | 22 March 2014, 20:01:26 UTC |
| e87c889 | Aidan Delaney | 22 March 2014, 19:57:18 UTC | Moved definition of print_usage to before its first use. | 22 March 2014, 19:57:18 UTC |
| 6db20de | andrewjpage | 17 February 2014, 16:30:48 UTC | Merge pull request #98 from andrewjpage/stats_missing_snps Stats missing snps | 17 February 2014, 16:30:48 UTC |
| 7c2bf65 | andrewjpage | 17 February 2014, 16:27:19 UTC | if theres no recombination bases return the number of snps outside recombination | 17 February 2014, 16:27:19 UTC |
| 1b7298a | andrewjpage | 17 February 2014, 15:09:39 UTC | set total snps before looking up recombinations | 17 February 2014, 15:09:39 UTC |
| c993048 | andrewjpage | 29 January 2014, 09:35:28 UTC | Merge pull request #97 from andrewjpage/nosupport update no support option in fastml | 29 January 2014, 09:35:28 UTC |
| 33d98a6 | andrewjpage | 29 January 2014, 09:35:07 UTC | update no support option in fastml | 29 January 2014, 09:35:07 UTC |
| 390a5e0 | andrewjpage | 11 November 2013, 11:47:49 UTC | Merge pull request #96 from andrewjpage/master move blocks inwards | 11 November 2013, 11:47:49 UTC |
| 8a4036b | andrewjpage | 08 November 2013, 12:14:54 UTC | move blocks inwards | 08 November 2013, 12:14:54 UTC |
| 8288a89 | andrewjpage | 08 November 2013, 11:18:10 UTC | Merge pull request #95 from andrewjpage/master define is starting tree method as static | 08 November 2013, 11:18:10 UTC |
| 9e0c82a | andrewjpage | 08 November 2013, 11:17:35 UTC | define is starting tree method as static | 08 November 2013, 11:17:35 UTC |
| de10bba | andrewjpage | 19 September 2013, 08:48:38 UTC | Merge pull request #94 from andrewjpage/master starting tree needed to come from args | 19 September 2013, 08:48:38 UTC |
| 1bb9ae0 | andrewjpage | 19 September 2013, 08:48:12 UTC | starting tree needed to come from args | 19 September 2013, 08:48:12 UTC |
| e8309de | andrewjpage | 19 August 2013, 09:45:09 UTC | Merge pull request #93 from andrewjpage/python_tests Python tests | 19 August 2013, 09:45:09 UTC |
| 1efc92d | andrewjpage | 19 August 2013, 09:38:39 UTC | test randomly stops prematurely since trees stop improving randomly | 19 August 2013, 09:38:39 UTC |
| f63f1d6 | andrewjpage | 16 August 2013, 15:04:33 UTC | cleanup tree from each iteration and check names are in tree and fasta | 16 August 2013, 15:04:33 UTC |
| 8f9a965 | andrewjpage | 16 August 2013, 14:34:13 UTC | use relative directory for bundled exec | 16 August 2013, 14:34:13 UTC |
| e93324a | andrewjpage | 16 August 2013, 13:26:22 UTC | Merge branch 'python_tests' of github.com:andrewjpage/gubbins into python_tests | 16 August 2013, 13:26:22 UTC |
| c9b6cec | andrewjpage | 16 August 2013, 13:25:42 UTC | move resize method so its available before use | 16 August 2013, 13:25:42 UTC |
| f7d26e1 | andrewjpage | 16 August 2013, 13:00:32 UTC | missing extra files from autoreconf | 16 August 2013, 13:00:32 UTC |
| 3d1f3a5 | andrewjpage | 16 August 2013, 12:46:08 UTC | autoreconf files | 16 August 2013, 12:46:08 UTC |
| 2a83d84 | andrewjpage | 16 August 2013, 10:46:17 UTC | update install instructions | 16 August 2013, 10:46:17 UTC |
| 068be2b | andrewjpage | 16 August 2013, 10:30:27 UTC | run configure step and install for fasttree | 16 August 2013, 10:30:27 UTC |
| 1e60b61 | andrewjpage | 16 August 2013, 10:22:52 UTC | Initial autoreconf | 16 August 2013, 10:22:52 UTC |
| bbb0d0d | andrewjpage | 16 August 2013, 10:22:36 UTC | python tests | 16 August 2013, 10:22:36 UTC |
| 4beadd0 | andrewjpage | 16 August 2013, 10:22:04 UTC | update configure and install doc | 16 August 2013, 10:22:04 UTC |
| 3bccaee | andrewjpage | 15 August 2013, 11:41:07 UTC | more tests for starting trees | 15 August 2013, 11:41:07 UTC |
| 1a39071 | andrewjpage | 13 August 2013, 15:45:08 UTC | all methods tested | 13 August 2013, 15:45:08 UTC |
| fd8cd1d | andrewjpage | 26 July 2013, 14:17:15 UTC | test using external bundle and deleting files | 26 July 2013, 14:17:15 UTC |
| 0f85c6d | andrewjpage | 26 July 2013, 11:07:38 UTC | test pairwise expected VCF and reconstructed fasta | 26 July 2013, 11:07:38 UTC |
| 5279176 | andrewjpage | 26 July 2013, 10:47:07 UTC | pairwise test | 26 July 2013, 10:47:07 UTC |
| 077651b | andrewjpage | 26 July 2013, 10:46:35 UTC | redundant get opt removed from fastml | 26 July 2013, 10:46:35 UTC |
| 1844cf1 | andrewjpage | 18 July 2013, 15:19:38 UTC | tests for reinserting gaps into sequence | 18 July 2013, 15:19:38 UTC |
| aacddf3 | andrewjpage | 17 July 2013, 09:58:49 UTC | test tree manipulation | 17 July 2013, 09:58:49 UTC |
| ad10510 | andrewjpage | 17 July 2013, 09:07:20 UTC | split tests into separate files | 17 July 2013, 09:07:20 UTC |
| d887a92 | andrewjpage | 16 July 2013, 13:48:26 UTC | tests for generating filenames | 16 July 2013, 13:48:26 UTC |
| 7c0a2b8 | andrewjpage | 16 July 2013, 13:24:31 UTC | class methods | 16 July 2013, 13:24:31 UTC |
| 531428d | andrewjpage | 16 July 2013, 11:25:31 UTC | test which and robinson_foulds_distance | 16 July 2013, 11:25:31 UTC |
| 68054d2 | andrewjpage | 10 July 2013, 12:36:17 UTC | nosetests | 16 July 2013, 09:45:45 UTC |
| bc454f5 | andrewjpage | 10 July 2013, 11:11:31 UTC | basic tests | 16 July 2013, 09:45:44 UTC |
| 78a8bc5 | andrewjpage | 10 July 2013, 10:08:32 UTC | reorganise python scripts into directory | 16 July 2013, 09:45:44 UTC |
| ff9ec07 | andrewjpage | 09 July 2013, 15:39:43 UTC | move python code to external module | 16 July 2013, 09:45:44 UTC |
| 23abbe5 | andrewjpage | 15 July 2013, 15:38:49 UTC | Merge pull request #92 from andrewjpage/master remove duplicate move | 15 July 2013, 15:38:49 UTC |
| 2b165e0 | andrewjpage | 15 July 2013, 15:38:20 UTC | dont move inwards twice | 15 July 2013, 15:38:20 UTC |
| 3b6212d | andrewjpage | 15 July 2013, 15:37:22 UTC | Merge pull request #91 from andrewjpage/master dont move in twice | 15 July 2013, 15:37:22 UTC |
| 06994cc | andrewjpage | 15 July 2013, 15:36:56 UTC | dont move inwards twice | 15 July 2013, 15:36:56 UTC |
| 0faea3e | andrewjpage | 10 July 2013, 15:17:49 UTC | Merge pull request #90 from andrewjpage/master typo in method, too many args | 10 July 2013, 15:17:49 UTC |
| b6a7449 | andrewjpage | 10 July 2013, 15:17:20 UTC | too many args | 10 July 2013, 15:17:20 UTC |
| 530839a | andrewjpage | 10 July 2013, 15:16:39 UTC | Merge pull request #89 from andrewjpage/master move end block in correct number of snps | 10 July 2013, 15:16:39 UTC |
| baf4220 | andrewjpage | 10 July 2013, 15:15:53 UTC | move end of block in correctly | 10 July 2013, 15:15:53 UTC |
| 5dcd091 | andrewjpage | 05 July 2013, 08:35:14 UTC | Merge pull request #88 from andrewjpage/master Span gaps | 05 July 2013, 08:35:14 UTC |
| 5811e55 | andrewjpage | 05 July 2013, 08:24:11 UTC | use child sequence for gaps when generating blocks | 05 July 2013, 08:24:11 UTC |
| 8b50f69 | andrewjpage | 04 July 2013, 15:23:20 UTC | off by one coord when creating blocks | 04 July 2013, 15:23:20 UTC |
| 3acc1d5 | andrewjpage | 04 July 2013, 15:23:07 UTC | print out neg log likelihood for a block | 04 July 2013, 15:23:07 UTC |
| df4ebb5 | andrewjpage | 04 July 2013, 09:25:19 UTC | Merge pull request #87 from andrewjpage/master translate snps and gaps to original genome space coords | 04 July 2013, 09:25:19 UTC |
| b3ff533 | andrewjpage | 03 July 2013, 14:26:20 UTC | translate snp and gaps to original genome space coords | 03 July 2013, 14:26:20 UTC |
| 0a9c845 | andrewjpage | 02 July 2013, 11:24:54 UTC | more efficiently find lower bound of window when close to beginning | 02 July 2013, 11:24:54 UTC |
| 4396e1a | andrewjpage | 02 July 2013, 09:54:59 UTC | Merge pull request #86 from andrewjpage/master extend blocks over gaps | 02 July 2013, 09:54:59 UTC |
| 18f4335 | andrewjpage | 02 July 2013, 09:54:17 UTC | extend blocks over gaps | 02 July 2013, 09:54:17 UTC |
| 7d60f03 | andrewjpage | 01 July 2013, 13:49:55 UTC | Merge pull request #85 from andrewjpage/master dont call methods and variables the same thing | 01 July 2013, 13:49:55 UTC |
| b81cda5 | andrewjpage | 01 July 2013, 13:49:28 UTC | dont call methods and variables the same thing | 01 July 2013, 13:49:28 UTC |
| 58740b7 | andrewjpage | 01 July 2013, 13:28:35 UTC | Merge pull request #84 from andrewjpage/master remove latest tree symlink if it exists, even if its broken | 01 July 2013, 13:28:35 UTC |
| bcd0ec6 | andrewjpage | 01 July 2013, 13:27:18 UTC | remove latest tree symlink if it exists, even if its broken | 01 July 2013, 13:27:18 UTC |
| eb0db7a | andrewjpage | 01 July 2013, 12:43:01 UTC | Merge pull request #83 from andrewjpage/master delete intermediate raxml files | 01 July 2013, 12:43:01 UTC |
| 8c0f4f4 | andrewjpage | 01 July 2013, 12:42:28 UTC | delete intermediate raxml files if they already exist | 01 July 2013, 12:42:28 UTC |
| db49772 | andrewjpage | 01 July 2013, 11:15:05 UTC | Merge pull request #82 from andrewjpage/master Eliminate memory leaks and uninitalised reads/writes | 01 July 2013, 11:15:05 UTC |
| 22a05b9 | andrewjpage | 01 July 2013, 11:14:04 UTC | Merge branch 'memory_copy' | 01 July 2013, 11:14:04 UTC |
| 9916dfe | andrewjpage | 01 July 2013, 11:07:12 UTC | free internal node array | 01 July 2013, 11:07:12 UTC |
| e066246 | andrewjpage | 01 July 2013, 11:01:50 UTC | clean up newick tree in correct order | 01 July 2013, 11:01:50 UTC |
| bfb37b5 | andrewjpage | 01 July 2013, 10:38:44 UTC | free the newick tree | 01 July 2013, 10:38:44 UTC |
| 5eaac09 | andrewjpage | 01 July 2013, 10:27:16 UTC | reenable freeing memory | 01 July 2013, 10:27:16 UTC |
| af88778 | andrewjpage | 01 July 2013, 10:05:29 UTC | use calloc over malloc | 01 July 2013, 10:05:29 UTC |
| 4add250 | andrewjpage | 01 July 2013, 09:54:36 UTC | use calloc instead of memcopy | 01 July 2013, 09:54:36 UTC |
| 9f505f0 | andrewjpage | 01 July 2013, 09:51:10 UTC | use calloc for parsing vcfs | 01 July 2013, 09:51:10 UTC |
| c6355cd | andrewjpage | 01 July 2013, 09:48:31 UTC | use calloc | 01 July 2013, 09:48:31 UTC |
