| 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 |
| 1a94fe7 | Connor McCoy | 30 January 2014, 23:35:41 UTC | Merge remote-tracking branch 'crosenth/master' | 30 January 2014, 23:35:41 UTC |
| dde6516 | Chris Rosenthal | 30 January 2014, 23:27:49 UTC | running cmalign-files with with a single thread (like pplacer in select) | 30 January 2014, 23:27:49 UTC |
| 254dc10 | Chris Rosenthal | 30 January 2014, 22:56:37 UTC | can set tmp dir using a TMPDIR env variable: http://docs.python.org/2/library/tempfile.html#tempfile.tempdir | 30 January 2014, 22:56:37 UTC |
| 4b35944 | Chris Rosenthal | 30 January 2014, 21:12:59 UTC | flush stdout and sterr before waiting for return code | 30 January 2014, 22:50:48 UTC |
| 0e43165 | Chris Rosenthal | 28 January 2014, 23:57:15 UTC | adding default of two threads per cmalign instance. Also, do not use the subprocess.wait() command with cmalign and futures. Causes deadlock. | 30 January 2014, 22:50:48 UTC |
| 730f1e5 | Chris Rosenthal | 24 January 2014, 23:34:02 UTC | writing each line of stdout, while good for memory consumption, looks funny as output. output should not be large so just reading all to memory is fine. | 30 January 2014, 22:50:48 UTC |
| ed3c49d | Chris Rosenthal | 24 January 2014, 23:06:32 UTC | tuning the logging down a notch. Also switched from subprocess.check_call to Popen to gain control over cmalign output. | 30 January 2014, 22:50:48 UTC |
| 293ba39 | Rosenthal | 13 January 2014, 19:05:03 UTC | Check for rppr before rerooting | 13 January 2014, 19:05:03 UTC |
| 3f5db47 | Connor McCoy | 09 January 2014, 23:06:10 UTC | Merge branch '04-infernal1.1' | 09 January 2014, 23:06:10 UTC |
| a3d9cee | Connor McCoy | 09 January 2014, 23:04:56 UTC | Check for cmalign 1.1 | 09 January 2014, 23:04:56 UTC |
| 87ca7a9 | Connor McCoy | 09 January 2014, 22:56:26 UTC | Add @nhoffman's fancy bootstrap script to README | 09 January 2014, 22:56:26 UTC |
| e595790 | Noah Hoffman | 09 January 2014, 22:22:37 UTC | define default number of cpus for cmalign using wrap.DEFAULT_CMALIGN_THREADS | 09 January 2014, 22:22:37 UTC |
| deb4699 | Noah Hoffman | 09 January 2014, 21:23:34 UTC | cmalign defaults to one cpu | 09 January 2014, 21:23:34 UTC |
| d03720b | Noah Hoffman | 09 January 2014, 20:23:00 UTC | drop MPI support | 09 January 2014, 20:23:00 UTC |
| 8d5d570 | Noah Hoffman | 31 December 2013, 01:19:39 UTC | remove debugging code | 31 December 2013, 01:19:39 UTC |
| 66aafe9 | Noah Hoffman | 31 December 2013, 01:10:33 UTC | - increment version to 0.0.2-dev - add CHANGES.txt - add bin/bootstrap.py (installs all dependencies in a virtualenv) - update url for tax2tree | 31 December 2013, 01:10:33 UTC |
| 3bc5118 | Noah Hoffman | 31 December 2013, 01:09:00 UTC | requires infernal 1.1 | 31 December 2013, 01:09:00 UTC |
| d6735ae | Noah Hoffman | 31 December 2013, 01:01:06 UTC | - add top-level run script for tests - save test output in output directories (to more easily ignore them) | 31 December 2013, 01:01:06 UTC |
| 6bf59c8 | Noah Hoffman | 31 December 2013, 00:05:58 UTC | update alignment model | 31 December 2013, 00:05:58 UTC |
| b8fe184 | Connor McCoy | 06 November 2013, 23:31:32 UTC | Merge pull request #5 from crosenth/master Assuming function name was desired here | 06 November 2013, 23:31:32 UTC |
| 8a5cc07 | Chris Rosenthal | 06 November 2013, 23:24:14 UTC | Assuming function name was desired here | 06 November 2013, 23:24:14 UTC |
| 44e88d6 | Connor McCoy | 22 August 2013, 21:56:44 UTC | Error on missing executable dependency | 22 August 2013, 22:01:08 UTC |
| ab9a6be | Connor McCoy | 22 August 2013, 21:29:07 UTC | Extract final set of sequences all at once | 22 August 2013, 22:01:08 UTC |
| 5163291 | Connor McCoy | 21 March 2013, 23:27:32 UTC | Update README.txt | 21 March 2013, 23:27:32 UTC |
| c568004 | Connor McCoy | 04 February 2013, 23:45:54 UTC | Bundle distribute; hack for multiprocessing bug `python setup.py test` fails in python 2.7.3 - http://bugs.python.org/issue15881. Importing multiprocessing/concurrent.futures resolves. | 04 February 2013, 23:45:59 UTC |
| 4321104 | Connor McCoy | 04 February 2013, 23:45:35 UTC | Add test suite for test_outliers | 04 February 2013, 23:45:35 UTC |
| dbec631 | Connor McCoy | 04 February 2013, 23:34:37 UTC | Merge branch '3-skip-pruning-option' | 04 February 2013, 23:34:37 UTC |
| 2eecab4 | Connor McCoy | 04 February 2013, 23:33:36 UTC | filter-outliers: change default --rare-taxon-action DROP -> KEEP | 04 February 2013, 23:33:36 UTC |
| 1334b55 | Connor McCoy | 04 February 2013, 20:05:48 UTC | Add option to skip pruning low-abundance sequences | 04 February 2013, 21:02:54 UTC |
| 82df9ec | Connor McCoy | 04 February 2013, 20:03:35 UTC | Remove old outlier filtering | 04 February 2013, 20:04:58 UTC |
| cf2bc89 | Connor McCoy | 04 February 2013, 19:46:18 UTC | pep8 fixes | 04 February 2013, 19:46:18 UTC |
| 569b41e | Connor McCoy | 04 February 2013, 19:32:05 UTC | Merge remote-tracking branch 'nhoffman/master' Closes pull request #1 | 04 February 2013, 19:32:05 UTC |
| 8ab243e | Noah Hoffman | 04 February 2013, 19:09:09 UTC | - reproduces original behavior of filter-outliers test | 04 February 2013, 19:09:09 UTC |
| 9e41152 | Noah Hoffman | 04 February 2013, 19:08:18 UTC | - fix bug when handling matrices of dim 2 | 04 February 2013, 19:08:18 UTC |
| 16cfec7 | Noah Hoffman | 04 February 2013, 06:19:13 UTC | - special handling for matrices of size 2,2 - simpler parsing of phylip distance matrix | 04 February 2013, 06:19:13 UTC |
| a5378e3 | Noah Hoffman | 01 February 2013, 07:24:16 UTC | use filter_sequences_numpy | 01 February 2013, 07:24:16 UTC |
| fe99f72 | Noah Hoffman | 01 February 2013, 06:51:19 UTC | add outliers.py and tests | 01 February 2013, 06:51:19 UTC |
| 303ff51 | Connor McCoy | 17 January 2013, 22:03:31 UTC | Slightly cleaner util.tempdir | 17 January 2013, 23:10:18 UTC |
| 2ab9b88 | Connor McCoy | 16 January 2013, 00:07:01 UTC | More sensitive cluster-refs | 16 January 2013, 00:07:01 UTC |
| 1a93717 | Connor McCoy | 05 January 2013, 00:19:36 UTC | Option for fill value when tax2tree does not assign | 05 January 2013, 00:19:36 UTC |
| ee85dfb | Connor McCoy | 19 December 2012, 22:37:23 UTC | Merge branch 'rename' | 19 December 2012, 22:37:23 UTC |
| 65aa017 | Connor McCoy | 19 December 2012, 22:28:27 UTC | Fall back on excel encoding I guess | 19 December 2012, 22:28:37 UTC |
| 40ea8d5 | Connor McCoy | 19 December 2012, 21:24:57 UTC | Option to log renames | 19 December 2012, 21:24:57 UTC |
| be3dca7 | Connor McCoy | 19 December 2012, 00:45:07 UTC | Initial implementation of `deenurp transfer-names` | 19 December 2012, 20:30:24 UTC |
| ecb6c4b | Connor McCoy | 18 December 2012, 18:39:11 UTC | Functions to add OTUs to refpkg | 18 December 2012, 18:39:11 UTC |
| b52c1c8 | Connor McCoy | 14 December 2012, 19:12:44 UTC | Merge branches 'lonely', 'blacklist' and 'whitelist' Conflicts: tests/search-select/run.sh | 14 December 2012, 19:12:44 UTC |
| 7d1b81c | Connor McCoy | 14 December 2012, 18:29:20 UTC | Allow configuring number of representatives And fix a bug where taxonomic nodes with n < n_reps failed. | 14 December 2012, 18:29:20 UTC |
| 16f7b76 | Connor McCoy | 12 December 2012, 18:12:09 UTC | Some formatting; documentation | 14 December 2012, 00:56:40 UTC |
| 8310e6d | Connor McCoy | 12 December 2012, 18:00:05 UTC | Quiet down the logging | 14 December 2012, 00:56:40 UTC |
| 2b2bed2 | Connor McCoy | 12 December 2012, 17:59:43 UTC | Optional logging in wrap.fasttree(...) | 14 December 2012, 00:56:40 UTC |
| 2d5df36 | Connor McCoy | 12 December 2012, 17:49:37 UTC | Concurrent execution for fill_lonely | 14 December 2012, 00:56:40 UTC |
| 0f6d8ea | Connor McCoy | 12 December 2012, 17:32:51 UTC | Initial work on fill_lonely.py | 14 December 2012, 00:56:40 UTC |
| 6eb2547 | Connor McCoy | 14 December 2012, 00:54:03 UTC | Update selection - only samples above threshold As of 5ed09219fc83915b36077c8cffc776d458617fe3, only the best hit *per group* is stored for each query sequence, so it's easy to calculate total weight for each cluster. | 14 December 2012, 00:56:16 UTC |
| 1d28862 | Connor McCoy | 13 December 2012, 19:54:51 UTC | README | 13 December 2012, 19:55:01 UTC |
| 595ea1f | Connor McCoy | 13 December 2012, 19:39:41 UTC | filter-outliers: handle errors, optional logging | 13 December 2012, 19:42:21 UTC |
| 5f98e23 | Connor McCoy | 12 December 2012, 19:24:43 UTC | Add --blacklist to `search-sequences` | 13 December 2012, 01:55:05 UTC |
| 36ef67f | Connor McCoy | 12 December 2012, 19:48:21 UTC | Add --whitelist to select-references | 13 December 2012, 01:54:32 UTC |
| 5ec8172 | Connor McCoy | 12 December 2012, 19:49:07 UTC | Define __contains__ for singletondefaultdict Fixes cases when sample map was not specified | 13 December 2012, 01:52:52 UTC |
| 4deca0f | Connor McCoy | 12 December 2012, 17:34:27 UTC | Merge branch 'cutoff-by-specimen' Conflicts: deenurp/select.py tests/search-select/run.sh | 13 December 2012, 01:52:52 UTC |
| 3498eaa | Connor McCoy | 30 November 2012, 18:41:10 UTC | Merge branch 'futures' into cutoff-by-specimen-futures Conflicts: deenurp/select.py | 13 December 2012, 01:42:16 UTC |
| 7d9af74 | Connor McCoy | 30 November 2012, 01:48:06 UTC | Export cache | 13 December 2012, 01:40:20 UTC |
| 764e1fb | Connor McCoy | 30 November 2012, 01:40:04 UTC | Commentin' | 13 December 2012, 01:40:19 UTC |
| 7a2dac4 | Connor McCoy | 30 November 2012, 01:21:37 UTC | Drop lock GIL should take care of this | 13 December 2012, 01:40:19 UTC |
| 01fc319 | Connor McCoy | 30 November 2012, 01:13:49 UTC | Use which from deenurp.util in test | 13 December 2012, 01:40:18 UTC |
| 81f588f | Connor McCoy | 30 November 2012, 00:56:16 UTC | No more MPI in filter-outliers | 13 December 2012, 01:40:18 UTC |
| 41b4e58 | Connor McCoy | 28 November 2012, 21:40:17 UTC | Working on hrefpkg | 13 December 2012, 01:40:17 UTC |
| ec8c0dd | Connor McCoy | 28 November 2012, 21:05:58 UTC | Futures requirements | 13 December 2012, 01:40:17 UTC |
| 9fdfb3e | Connor McCoy | 28 November 2012, 20:26:01 UTC | Trying out futures | 13 December 2012, 01:40:17 UTC |
| 8939c45 | Connor McCoy | 30 November 2012, 16:25:41 UTC | Allow orphan sequences for now | 13 December 2012, 01:40:16 UTC |
| 06728e2 | Connor McCoy | 30 November 2012, 00:02:54 UTC | Consistent terminology Sample instead of specimen | 13 December 2012, 01:40:16 UTC |
| 5ed0921 | Connor McCoy | 29 November 2012, 23:07:27 UTC | Only store one hit per group | 13 December 2012, 01:40:15 UTC |
| 085d2e8 | Connor McCoy | 29 November 2012, 22:23:32 UTC | Per-sample weight | 13 December 2012, 01:40:15 UTC |
| 5eff4fd | Connor McCoy | 29 November 2012, 21:48:52 UTC | Search working | 13 December 2012, 01:40:15 UTC |
| 11616c9 | Connor McCoy | 04 December 2012, 00:49:01 UTC | Add rppr_min_adcl_tree | 04 December 2012, 00:50:37 UTC |
| a70e6e9 | Connor McCoy | 30 November 2012, 00:12:08 UTC | Fix audit | 30 November 2012, 01:29:13 UTC |
| 856724f | Connor McCoy | 29 November 2012, 23:07:27 UTC | Only store one hit per group Cleans up some queries | 30 November 2012, 01:29:13 UTC |
| 63fe7c0 | Connor McCoy | 29 November 2012, 23:07:04 UTC | Use uclust instead of usearch | 30 November 2012, 01:29:13 UTC |
| de64688 | Connor McCoy | 29 November 2012, 21:49:27 UTC | Species-level tax_id for clustering | 30 November 2012, 01:29:12 UTC |
| f2f880f | Connor McCoy | 28 November 2012, 21:50:45 UTC | support specifying deenurp | 28 November 2012, 22:24:24 UTC |
| b6950c1 | Connor McCoy | 28 November 2012, 19:36:22 UTC | Test for search | 28 November 2012, 22:24:24 UTC |
| 085868a | Connor McCoy | 28 November 2012, 19:20:25 UTC | hrefpkg test | 28 November 2012, 22:24:24 UTC |
| cdb7c94 | Connor McCoy | 28 November 2012, 22:21:02 UTC | Support naming temporary reference packages | 28 November 2012, 22:24:24 UTC |
| 1990e42 | Connor McCoy | 28 November 2012, 22:19:56 UTC | README updates | 28 November 2012, 22:24:23 UTC |
| facf077 | Connor McCoy | 28 November 2012, 22:07:14 UTC | Fall back on single-threaded FastTree, cmalign | 28 November 2012, 22:24:23 UTC |
| beee5f3 | Connor McCoy | 28 November 2012, 20:07:14 UTC | Tweak defaults for MPI | 28 November 2012, 22:24:23 UTC |
| 03f3ef1 | Connor McCoy | 28 November 2012, 18:14:56 UTC | Add test for as_refpkg | 28 November 2012, 22:24:23 UTC |
| 2f32d33 | Connor McCoy | 28 November 2012, 17:20:51 UTC | More informative name | 28 November 2012, 22:24:23 UTC |
| 2dc2472 | Connor McCoy | 28 November 2012, 16:46:47 UTC | Add `--output-dir` flag to `hrefpkg-build` | 28 November 2012, 22:24:23 UTC |
| 8851047 | Connor McCoy | 27 November 2012, 15:21:55 UTC | Non-editable checkouts | 27 November 2012, 15:31:22 UTC |
| d41994e | Connor McCoy | 27 November 2012, 15:21:55 UTC | Update peasel | 27 November 2012, 15:21:55 UTC |
| b6ce0f1 | Connor McCoy | 19 November 2012, 18:23:23 UTC | Open files with compression based on extension | 19 November 2012, 23:38:42 UTC |
| a8af073 | Connor McCoy | 16 November 2012, 23:14:43 UTC | Use new is_valid column to classification status | 17 November 2012, 00:01:33 UTC |
| a6082c5 | Connor McCoy | 07 November 2012, 20:17:50 UTC | Use RDP annotation of type strain. | 07 November 2012, 20:17:50 UTC |
| f98b71c | Connor McCoy | 01 November 2012, 20:52:14 UTC | Use temporary SSI for fetching query seqs Still indexing-in-place for reference sequences. | 01 November 2012, 23:51:31 UTC |
| 8f8b01c | Connor McCoy | 25 October 2012, 22:54:51 UTC | Convert from unicode. | 25 October 2012, 22:54:51 UTC |
| 51b36f1 | Connor McCoy | 25 October 2012, 22:54:44 UTC | Command line parameter for grouping field in reference sequences | 25 October 2012, 22:54:44 UTC |
