| 49722f7 | Noah Hoffman | 19 February 2015, 21:46:45 UTC | Merge branch 'filter-with-clusters' of github.com:fhcrc/deenurp into filter-with-clusters | 19 February 2015, 21:46:45 UTC |
| 55588bb | Noah Hoffman | 19 February 2015, 21:36:26 UTC | update docstring AND changelog | 19 February 2015, 21:36:26 UTC |
| 2967a10 | Noah Hoffman | 16 February 2015, 04:27:57 UTC | fix name of README in manifest | 16 February 2015, 04:27:57 UTC |
| 8e9ce88 | Noah Hoffman | 12 February 2015, 21:47:29 UTC | add option for cluster type | 12 February 2015, 21:47:29 UTC |
| 97fb232 | Noah Hoffman | 12 February 2015, 21:47:11 UTC | remove print statements | 12 February 2015, 21:47:11 UTC |
| b969698 | Noah Hoffman | 12 February 2015, 00:50:05 UTC | set random seed for MDS | 12 February 2015, 00:50:05 UTC |
| 85f7d73 | Noah Hoffman | 11 February 2015, 01:17:46 UTC | outliers.mds() handles matrix with all zeros add scikit-learn to requirements.txt | 11 February 2015, 01:17:46 UTC |
| 7c0bbba | Noah Hoffman | 11 February 2015, 00:31:44 UTC | ask travis for longer timeout interval | 11 February 2015, 00:31:44 UTC |
| 08a71c4 | Noah Hoffman | 11 February 2015, 00:27:52 UTC | add outliers.mds() | 11 February 2015, 00:27:52 UTC |
| df0d256 | Noah Hoffman | 10 February 2015, 23:57:06 UTC | fully implemented outlier detection by clustering test suites are collected automatically | 10 February 2015, 23:57:06 UTC |
| e72e1d0 | Noah Hoffman | 09 February 2015, 22:22:23 UTC | configure logging in setup.py (can control verbosity in unit tests) | 09 February 2015, 22:22:23 UTC |
| 0b15edc | Noah Hoffman | 06 February 2015, 05:37:46 UTC | add "travis_wait" to avoid timeout | 06 February 2015, 05:37:46 UTC |
| 025c3d3 | Noah Hoffman | 06 February 2015, 05:11:15 UTC | install scipy system dependencies during travis setup | 06 February 2015, 05:11:15 UTC |
| 81f1011 | Noah Hoffman | 06 February 2015, 01:09:07 UTC | - remove filter_outliers --log option - simplify params of filter_outliers() and filter_worker() | 06 February 2015, 01:09:07 UTC |
| 4e0dc28 | Noah Hoffman | 06 February 2015, 01:06:58 UTC | - outliers.outliers() no longer has special handling for a small matrix - add outliers.outliers_by_cluster() implementing filter by clustering - add outliers.scaled_radius() | 06 February 2015, 01:06:58 UTC |
| 33c1f2b | Noah Hoffman | 05 February 2015, 21:55:51 UTC | add outliers.find_cluster_medoids() and outliers.choose_clusters() | 05 February 2015, 21:55:51 UTC |
| decf435 | Noah Hoffman | 05 February 2015, 19:00:00 UTC | add scipy_clusters | 05 February 2015, 19:00:00 UTC |
| 97c538d | Noah Hoffman | 03 February 2015, 01:18:57 UTC | add find_medoid | 03 February 2015, 01:18:57 UTC |
| 1cc89c3 | Noah Hoffman | 03 February 2015, 00:46:56 UTC | remove support for usearch | 03 February 2015, 00:50:47 UTC |
| b185812 | Noah Hoffman | 02 February 2015, 23:38:26 UTC | defines package version using 'git describe --tags --dirty' | 02 February 2015, 23:38:26 UTC |
| 5efd9ea | Noah Hoffman | 08 January 2015, 18:48:56 UTC | increment version of vsearch | 08 January 2015, 18:48:56 UTC |
| 2c40c78 | Noah Hoffman | 06 January 2015, 00:11:06 UTC | fix typo and update docstring | 06 January 2015, 00:11:06 UTC |
| 1b9f5c1 | Noah Hoffman | 15 December 2014, 18:36:49 UTC | add ``deenurp pairwise-distances`` | 15 December 2014, 18:36:49 UTC |
| 9cdb560 | Noah Hoffman | 15 December 2014, 18:36:36 UTC | update vsearch version | 15 December 2014, 18:36:36 UTC |
| 564876d | Noah Hoffman | 15 December 2014, 18:36:18 UTC | actually run tests for filter-outliers | 15 December 2014, 18:36:18 UTC |
| cb1d5ed | Noah Hoffman | 15 December 2014, 18:08:44 UTC | use first line of docstring for top-level help text | 15 December 2014, 18:08:44 UTC |
| 4096a99 | Noah Hoffman | 09 December 2014, 19:17:17 UTC | check vsearch version use vsearch --allpairs_global | 09 December 2014, 19:17:17 UTC |
| 47edf9e | Noah Hoffman | 09 December 2014, 18:28:58 UTC | - be more consistent in the use of configuration variables - update filter-outliers command line options | 09 December 2014, 18:28:58 UTC |
| 151b3cc | Noah Hoffman | 09 December 2014, 18:28:01 UTC | handle nan in distance matrix when identifying outliers | 09 December 2014, 18:28:01 UTC |
| e990db6 | Noah Hoffman | 07 December 2014, 06:48:46 UTC | - installs vsearch - filter_outliers can use vsearch as an aligner - bootstrap.sh downloads virtualenv source only if necessary | 07 December 2014, 06:48:46 UTC |
| d4eb589 | Noah Hoffman | 06 December 2014, 21:50:44 UTC | add wrap.vsearch_allpairs_files | 06 December 2014, 21:50:44 UTC |
| 0088be3 | Noah Hoffman | 05 December 2014, 23:25:23 UTC | a few comments | 05 December 2014, 23:25:23 UTC |
| 2dfcd82 | Noah Hoffman | 05 December 2014, 06:29:20 UTC | skip usearch tests if not available | 05 December 2014, 06:29:20 UTC |
| 2e7a368 | Noah Hoffman | 05 December 2014, 05:44:08 UTC | add pandas, update other requirements | 05 December 2014, 05:44:08 UTC |
| e0befd4 | Noah Hoffman | 05 December 2014, 00:58:17 UTC | update changelog don't run filter_outliers with usearch unless usearch6 is installed | 05 December 2014, 00:58:17 UTC |
| 866a6df | Noah Hoffman | 05 December 2014, 00:47:30 UTC | results are accumulated as pandas dataframes add 'deenurp filter-outliers --detailed-seqinfo' | 05 December 2014, 00:47:30 UTC |
| c4b83f6 | Noah Hoffman | 04 December 2014, 21:34:46 UTC | filter_outliers returns a pandas dataframe | 04 December 2014, 21:34:46 UTC |
| 2268cbc | Noah Hoffman | 04 December 2014, 18:48:21 UTC | parse usearch output for allpairs | 04 December 2014, 18:48:21 UTC |
| 60234c5 | Noah Hoffman | 27 November 2014, 01:13:35 UTC | in the midst of implementing usearch pairwise distances (realizing that not all pairwise distances are returned) | 27 November 2014, 01:13:35 UTC |
| bab02ad | Noah Hoffman | 26 November 2014, 21:04:54 UTC | detect usearch executable and version and | 26 November 2014, 21:04:54 UTC |
| 69eecd8 | Noah Hoffman | 26 November 2014, 17:50:10 UTC | dispatch dmat creation to a different function for each aligner | 26 November 2014, 17:50:10 UTC |
| 4581a18 | Noah Hoffman | 24 November 2014, 19:13:42 UTC | update version string | 24 November 2014, 19:13:42 UTC |
| b810de0 | Noah Hoffman | 24 November 2014, 18:42:58 UTC | filter-outliers can use muscle | 24 November 2014, 18:42:58 UTC |
| 8231fc1 | Noah Hoffman | 18 November 2014, 06:33:15 UTC | add test for filter_sequences formatting | 18 November 2014, 06:33:15 UTC |
| 2a86d06 | Noah Hoffman | 18 November 2014, 06:16:42 UTC | install muscle | 18 November 2014, 06:16:42 UTC |
| 87cad79 | Noah Hoffman | 18 November 2014, 01:04:04 UTC | Revert "tax2tree now specifies its own dependencies" This reverts commit 1ffbb71aa9a25eb615b904a93fb01c2d517d5a3a. | 18 November 2014, 01:04:04 UTC |
| 834ce6a | Noah Hoffman | 18 November 2014, 01:04:04 UTC | Revert "specifying required installs outside tax2tree" This reverts commit 09317130e4e854bb86e8a86696da77d64e725fe3. | 18 November 2014, 01:04:04 UTC |
| d977fe3 | Noah Hoffman | 18 November 2014, 01:04:03 UTC | Revert "include wheel location when installing setup.py" This reverts commit 6cc17578588ea783bf465217fdd1bdfe8f87f5df. | 18 November 2014, 01:04:03 UTC |
| 744c232 | Noah Hoffman | 18 November 2014, 01:03:56 UTC | Revert "adding crosenth to travis email list" This reverts commit c9c80cf1b846291f5b56def3bd75dbf09c2a8544. | 18 November 2014, 01:03:56 UTC |
| 4b08d14 | Noah Hoffman | 18 November 2014, 01:03:52 UTC | Revert "installation problem in scikit-bio, need to install numpy here" This reverts commit 94f6b8771ec37948f708b62753544db8625376f9. | 18 November 2014, 01:03:52 UTC |
| 4c5a3f0 | Noah Hoffman | 18 November 2014, 01:03:49 UTC | Revert "ignore comments in requirements.txt file" This reverts commit 398408ca8a006d55c24961d4def8240a49857057. | 18 November 2014, 01:03:49 UTC |
| 3d4cafa | Noah Hoffman | 18 November 2014, 01:01:39 UTC | Revert "install numpy sys dependencies first" This reverts commit 6d52cb71b944d28fd38abed0b92abc95ccc4605d. | 18 November 2014, 01:01:39 UTC |
| 6d52cb7 | Chris Rosenthal | 14 November 2014, 22:37:09 UTC | install numpy sys dependencies first | 14 November 2014, 22:37:09 UTC |
| 398408c | Chris Rosenthal | 14 November 2014, 18:56:51 UTC | ignore comments in requirements.txt file | 14 November 2014, 18:56:51 UTC |
| 94f6b87 | Chris Rosenthal | 14 November 2014, 18:22:34 UTC | installation problem in scikit-bio, need to install numpy here | 14 November 2014, 18:22:34 UTC |
| c9c80cf | Chris Rosenthal | 14 November 2014, 18:13:50 UTC | adding crosenth to travis email list | 14 November 2014, 18:13:50 UTC |
| 6cc1757 | Chris Rosenthal | 14 November 2014, 00:04:32 UTC | include wheel location when installing setup.py | 14 November 2014, 00:04:32 UTC |
| 0931713 | Chris Rosenthal | 13 November 2014, 23:23:27 UTC | specifying required installs outside tax2tree | 13 November 2014, 23:23:27 UTC |
| 1ffbb71 | Chris Rosenthal | 13 November 2014, 23:22:45 UTC | tax2tree now specifies its own dependencies | 13 November 2014, 23:22:45 UTC |
| 414cc9e | Noah Hoffman | 16 October 2014, 21:37:30 UTC | remove reference to r script | 16 October 2014, 21:37:30 UTC |
| 7368bd7 | Noah Hoffman | 16 October 2014, 20:31:39 UTC | don't require input seq_info and fasta file to be the same length | 16 October 2014, 20:31:39 UTC |
| 34dfcae | Noah Hoffman | 10 October 2014, 22:18:53 UTC | explicitly name output files | 10 October 2014, 22:18:53 UTC |
| 462bbf1 | Noah Hoffman | 10 October 2014, 22:12:27 UTC | pep8 | 10 October 2014, 22:12:27 UTC |
| 7f03172 | Noah Hoffman | 19 September 2014, 05:57:40 UTC | increment version | 19 September 2014, 05:57:40 UTC |
| 2c06b92 | Noah Hoffman | 19 September 2014, 05:20:15 UTC | suppress FastTree messages in absence of an error | 19 September 2014, 05:20:15 UTC |
| 9775b7b | Noah Hoffman | 19 September 2014, 05:19:34 UTC | docs | 19 September 2014, 05:19:34 UTC |
| 29f0ecd | Noah Hoffman | 19 September 2014, 04:10:37 UTC | be less verbose | 19 September 2014, 04:10:37 UTC |
| f3eb46f | Noah Hoffman | 18 September 2014, 23:55:16 UTC | work on docs | 18 September 2014, 23:55:16 UTC |
| 928482e | Noah Hoffman | 18 September 2014, 23:54:02 UTC | trying to debug travis-specific errors | 18 September 2014, 23:54:02 UTC |
| 0e97a45 | Noah Hoffman | 18 September 2014, 23:18:54 UTC | formatting | 18 September 2014, 23:18:54 UTC |
| 146c40c | Noah Hoffman | 18 September 2014, 22:51:02 UTC | trying to resolve exception raised in tests for filter_outliers.py | 18 September 2014, 22:51:02 UTC |
| 9ee6a4c | Noah Hoffman | 11 August 2014, 21:41:18 UTC | provide data types for command line options | 11 August 2014, 21:41:18 UTC |
| 8054de7 | Noah Hoffman | 11 August 2014, 21:29:01 UTC | - make function arguments more consistent with command line options - fix sanity check comparing values for options in search_sequences - re-raise exception with traceback in filter_outliers | 11 August 2014, 21:29:01 UTC |
| de061a2 | Noah Hoffman | 11 August 2014, 17:49:24 UTC | formatting | 11 August 2014, 17:49:24 UTC |
| 8097150 | Noah Hoffman | 08 August 2014, 00:25:37 UTC | remove .ssi file if it exists | 08 August 2014, 00:25:37 UTC |
| bd608c5 | Noah Hoffman | 08 August 2014, 00:10:00 UTC | pep8 | 08 August 2014, 00:10:00 UTC |
| 2dacc75 | Noah Hoffman | 08 August 2014, 00:07:08 UTC | pep8 | 08 August 2014, 00:07:08 UTC |
| b2e7c74 | Noah Hoffman | 08 August 2014, 00:06:58 UTC | update docstring | 08 August 2014, 00:06:58 UTC |
| 690d648 | Noah Hoffman | 07 August 2014, 23:34:34 UTC | - define constants for default values of some numeric options - comments and docstrings clarifying search_sequences | 07 August 2014, 23:34:34 UTC |
| bd2a0cc | Noah Hoffman | 24 July 2014, 22:41:02 UTC | pep8, comments | 24 July 2014, 22:41:02 UTC |
| 1d3541f | Noah Hoffman | 24 July 2014, 21:59:09 UTC | pep8 | 24 July 2014, 21:59:09 UTC |
| 6054f4d | Noah Hoffman | 24 July 2014, 20:14:21 UTC | rename README | 24 July 2014, 20:14:21 UTC |
| 7887006 | Noah Hoffman | 24 July 2014, 19:01:21 UTC | add option to install packages from wheels | 24 July 2014, 19:01:21 UTC |
| c88a767 | Noah Hoffman | 26 June 2014, 23:53:27 UTC | - bootstrap.sh checks pplacer build version - travis notifies Noah instead of Connor | 26 June 2014, 23:53:27 UTC |
| 1642211 | Noah Hoffman | 24 March 2014, 21:58:11 UTC | Comments | 24 March 2014, 21:58:11 UTC |
| 370cd18 | Chris Rosenthal | 10 March 2014, 22:02:47 UTC | deenurp basedir located directly below bin | 10 March 2014, 22:02:47 UTC |
| 7299875 | Noah Hoffman | 07 February 2014, 00:06:12 UTC | bootstrap.sh installs raxml | 07 February 2014, 00:06:12 UTC |
| 92a9ef5 | Noah Hoffman | 06 February 2014, 19:44:03 UTC | Merge pull request #12 from fhcrc/all-cores Make multithreaded tasks use all cores by default | 06 February 2014, 19:44:03 UTC |
| b2f141f | Connor McCoy | 05 February 2014, 23:07:22 UTC | exit on error | 05 February 2014, 23:07:22 UTC |
| 813a525 | Connor McCoy | 05 February 2014, 22:55:39 UTC | Default to all CPUs in multithreaded sections | 05 February 2014, 23:01:49 UTC |
| 6576006 | Connor McCoy | 05 February 2014, 22:42:47 UTC | bootstrap fixes; run tests in travis | 05 February 2014, 23:01:48 UTC |
| b5d74f2 | Connor McCoy | 05 February 2014, 22:50:14 UTC | Default to 1 thread for cmalign | 05 February 2014, 23:01:48 UTC |
| afb1117 | Connor McCoy | 05 February 2014, 22:35:49 UTC | run integration tests | 05 February 2014, 22:35:49 UTC |
| 1f31dd4 | Connor McCoy | 05 February 2014, 22:26:22 UTC | tweak | 05 February 2014, 22:26:22 UTC |
| e9820e1 | Connor McCoy | 05 February 2014, 22:11:21 UTC | travis | 05 February 2014, 22:11:21 UTC |
| 8d9e206 | Connor McCoy | 05 February 2014, 21:55:20 UTC | bump | 05 February 2014, 21:55:20 UTC |
| ab148ec | Connor McCoy | 05 February 2014, 21:52:32 UTC | Merge remote-tracking branch 'origin/bump-to-002' | 05 February 2014, 21:52:32 UTC |
| 0879bc3 | Noah Hoffman | 05 February 2014, 20:33:54 UTC | - bump version number to 0.0.2 - update requirements - bootstrap script can be run from arbitrary working directory | 05 February 2014, 20:33:54 UTC |
| 416306e | Connor McCoy | 31 January 2014, 15:28:32 UTC | Merge pull request #10 from crosenth/master cpu not threads | 31 January 2014, 15:28:32 UTC |
| bae8f4b | Chris Rosenthal | 31 January 2014, 01:45:36 UTC | cpu not threads | 31 January 2014, 01:45:36 UTC |
